Methylobacterium Compositions and Plants, Plant Parts and Seeds Coated Therewith

ABSTRACT

The present invention provides both compositions comprising  Methylobacterium  and compositions comprising  Methylobacterium  that are depleted of substances that promote growth of resident microorganisms on a lettuce plant or seed. Also provided are methods for improving lettuce production, methods of making the compositions, and methods of treating a lettuce plant or seed with the compositions comprising  Methylobacterium.

CROSS REFERENCE TO RELATED APPLICATIONS

This patent application is a Divisional of U.S. patent application Ser.No. 15/101,374, filed Jun. 2, 2016, which is a 35 U.S.C. § 371 USnational stage application of International Patent ApplicationPCT/US2014/068558, filed Dec. 4, 2014 and incorporated herein byreference in its entirety, which claims the benefit of U.S. ProvisionalPatent Application No. 61/954,840, filed Mar. 18, 2014, and U.S.Provisional Patent Application No., 61/911,516, filed Dec. 4, 2013,which are each incorporated herein by reference.

SEQUENCE LISTING STATEMENT

A sequence listing containing the file named 53907⁻179989_SL.txt whichis 15,167,424 bytes (measured in MS-Windows®) and created on Jan. 2,2019, comprises 10,250 sequences, is provided herewith via the USPTO'sEFS system, and is incorporated herein by reference in its entirety.

BACKGROUND

One-carbon organic compounds such as methane and methanol are foundextensively in nature, and are utilized as carbon sources by bacteriaclassified as methanotrophs and methylotrophs. Methanotrophic bacteriainclude species in the genera Methylobacter, Methylomonas,Methylomicrobium, Methylococcus, Methylosinus, Methylocystis,Methylosphaera, Methylocaldum, and Methylocella (Lidstrom, 2006).Methanotrophs possess the enzyme methane monooxygenase, thatincorporates an atom of oxygen from O₂ into methane, forming methanol.All methanotrophs are obligate one-carbon utilizers that are unable touse compounds containing carbon-carbon bonds. Methylotrophs, on theother hand, can also utilize more complex organic compounds, such asorganic acids, higher alcohols, sugars, and the like. Thus,methylotrophic bacteria are facultative methylotrophs. Methylotrophicbacteria include species in the genera Methylobacterium, Hyphomicrobium,Methylophilus, Methylobacillus, Methylophaga, Aminobacter,Methylorhabdus, Methylopila, Methylosulfonomonas, Marinosulfonomonas,Paracoccus, Xanthobacter, Ancylobacter (also known as Microcyclus),Thiobacillus, Rhodopseudomonas, Rhodobacter, Acetobacter, Bacillus,Mycobacterium, Arthobacter, and Nocardia (Lidstrom, 2006).

Most methylotrophic bacteria of the genus Methylobacterium arepink-pigmented. They are conventionally referred to as PPFM bacteria,being pink-pigmented facultative methylotrophs. Green (2005, 2006)identified twelve validated species in the genus Methylobacterium,specifically M. aminovorans, M. chloromethanicum, M. dichloromethanicum,M. extorquens, M. fujisawaense, M. mesophilicum, M. organophilum, M.radiotolerans, M. rhodesianum, M. rhodinum, M. thiocyanatum, and M.zatmanii. However, M. nidulans is a nitrogen-fixing Methylobacteriumthat is not a PPFM (Sy et al., 2001). Methylobacterium are ubiquitous innature, being found in soil, dust, fresh water, sediments, and leafsurfaces, as well as in industrial and clinical environments (Green,2006).

SUMMARY

Provided herein are compositions comprising Methylobacterium that aredepleted of substances that promote growth of resident bacteria on theplant or seed, compositions comprising a solid substance with adherentMethylobacterium grown thereon or an emulsion having Methylobacteriumgrown therein, compositions comprising certain Methylobacterium strains,methods of using the compositions to improve lettuce production, andmethods of making the compositions. Such compositions are in certaininstances referred to herein as simply “Methylobacterium-containingcompositions”. In certain embodiments, the Methylobacterium in thecomposition or that is used is strain NLS0020, NLS0066, NLS0017,NLS0065, NLS0089, NLS0042, or NLS0068. In certain embodiments, theMethylobacterium in the composition or that is used is Methylobacteriumis selected from the group consisting of NLS0017 (NRRL B-50931), NLS0020(NRRL B-50930), NLS0021 (NRRL B-50939), NLS0037 (NRRL B-50941), NLS0038(NRRL B-50942), NLS0042 (NRRL B-50932), NLS0046 (NRRL B-50929), NLS0062(NRRL B-50937), NLS0064 (NRRL B-50938), NLS0065 (NRRL B-50935), NLS0066(NRRL B-50940), NLS0068 (NRRL B-50934), NLS0069 (NRRL B-50936), NLS0089(NRRL B-50933), and derivatives thereof. In certain embodiments, theMethylobacterium in the composition or that is used is aMethylobacterium that has at least one gene encoding a protein that isorthologous to a protein having an amino acid sequence of SEQ ID NO:1-5125. In certain embodiments, the Methylobacterium has at least onegene encoding a protein that is orthologous to a reference protein ofTable 7. In certain embodiments, the Methylobacterium sp. can contain atleast one gene encoding a protein that is orthologous to a referenceprotein having the amino acid sequence of 13, 14, 23, 27, 28, 30, 40,43, 44, 51, 52, 57, 76, 85, 127, 197, 198, 199, 1094, 1100, 1106, 1114,1116, 1117, 1120, 1180, 2180, 2190, 2463, 2467, 2468, 2471, 2510, 2515,2676, 2971, 3357, 3370, 3372, 3394, 3427, 3429, 3430, 3950, 3952, 3968,3987, 3996, 4004, 4006, and/or 4067 of Table 7. In certain embodimentsthe Methylobacterium has at least one gene encoding a protein that isorthologous to a reference protein is selected from the group consistingof SEQ ID NO: 13, 14, 23, 1094, 1100, 1106, 2467, 2468, 3357, 3370,and/or 3968. In certain embodiments the Methylobacterium has at leastone gene encoding a protein that is orthologous to a reference proteinis selected from the group consisting of SEQ ID NO: 1100, 1116, 2471and/or 3950. In certain embodiments, the Methylobacterium in thecomposition or that is used is strain NLS0020, NLS0066, NLS0017,NLS0065, or NLS0089 and the composition is used to treat a lettuce seed.

Methods for improving lettuce production comprising applying a coatingor partial coating of a composition comprising Methylobacterium to alettuce plant, a part thereof, or to a lettuce seed, wherein saidcomposition comprises: (a) a solid substance with adherentMethylobacterium grown thereon; (b) an emulsion having Methylobacteriumgrown therein; (c) certain Methylobacterium strains selected from thegroup consisting of NLS0017 (NRRL B-50931), NLS0020 (NRRL B-50930),NLS0021 (NRRL B-50939), NLS0037 (NRRL B-50941), NLS0038 (NRRL B-50942),NLS0042 (NRRL B-50932), NLS0046 (NRRL B-50929), NLS0062 (NRRL B-50937),NLS0064 (NRRL B-50938), NLS0065 (NRRL B-50935), NLS0066 (NRRL B-50940),NLS0068 (NRRL B-50934), NLS0069 (NRRL B-50936), NLS0089 (NRRL B-50933),and derivatives thereof and an agriculturally acceptable adjuvant,excipient, or combination thereof; or (d) a Methylobacterium that has atleast one gene encoding at least one protein that is orthologous to aprotein having an amino acid sequence of SEQ ID NO: 1-5125 and anagriculturally acceptable adjuvant, excipient, or combination thereof;and wherein said lettuce plant or lettuce plant grown from said seedexhibits a trait improvement selected from the group consisting of anincreased rate of leaf growth, an increased rate of root growth,increased total biomass production, increased seed yield, decreasedcycle time, and combinations thereof when compared to an untreatedcontrol lettuce plant or a control lettuce plant grown from an untreatedseed are provided herein. In certain embodiments, the compositioncomprises Methylobacterium at a titer of about 1×10⁶ CFU/gm to about1×10¹⁴ CFU/gm for a solid composition or at a titer of about 1×10⁶CFU/mL to about 1×10¹¹ CFU/mL for a liquid composition containing thesolid substance or for the emulsion. In certain embodiments, theMethylobacterium has at least one gene encoding at least one proteinthat is orthologous to a protein having an amino acid sequence of SEQ IDNO: 1-5125. In certain embodiments, the Methylobacterium has at leastone gene encoding a protein that is orthologous to a reference proteinof Table 7. In certain embodiments, the Methylobacterium sp. can containat least one gene encoding a protein that is orthologous to a referenceprotein having the amino acid sequence of 13, 14, 23, 27, 28, 30, 40,43, 44, 51, 52, 57, 76, 85, 127, 197, 198, 199, 1094, 1100, 1106,1114,1116, 1117, 1120, 1180, 2180, 2190, 2463, 2467, 2468, 2471, 2510,2515, 2676, 2971, 3357, 3370, 3372, 3394, 3427, 3429, 3430, 3950, 3952,3968, 3987, 3996, 4004, 4006, and/or 4067 of Table 7. In certainembodiments the Methylobacterium has at least one gene encoding aprotein that is orthologous to a reference protein is selected from thegroup consisting of SEQ ID NO: 13, 14, 23, 1094, 1100, 1106, 2467, 2468,3357, 3370, and/or 3968. In certain embodiments the Methylobacterium hasat least one gene encoding a protein that is orthologous to a referenceprotein is selected from the group consisting of SEQ ID NO: 1100, 1116,2471 and/or 3950. In certain embodiments, the Methylobacterium in thecomposition or that is used is selected from the group consisting ofNLS0017 (NRRL B-50931), NLS0020 (NRRL B-50930), NLS0021 (NRRL B-50939),NLS0037 (NRRL B-50941), NLS0038 (NRRL B-50942), NLS0042 (NRRL B-50932),NLS0046 (NRRL B-50929), NLS0062 (NRRL B-50937), NLS0064 (NRRL B-50938),NLS0065 (NRRL B-50935), NLS0066 (NRRL B-50940), NLS0068 (NRRL B-50934),NLS0069 (NRRL B-50936), NLS0089 (NRRL B-50933), and derivatives thereof.In certain embodiments, the Methylobacterium in the composition or thatis used is selected from the group consisting of NLS0017, NLS0037,NLS0066, NLS0020, NLS0042, NLS0065, NLS0089, NLS0046, NLS0021. NLS0069,NLS0068, NLS0064, NLS0062, NLS0038, and derivatives thereof. In certainembodiments, the Methylobacterium has at least one polymorphic DNAelement that is present in at least one Methylobacterium strain selectedfrom the group consisting of NLS0020, NLS0066, NLS0017, NLS0065,NLS0089, NLS0042, and NLS0068 provided herein that improve lettuceproduction but that is absent from Methylobacterium sp. that do notimprove lettuce production. In certain embodiments, the composition isapplied to a lettuce seed and the least one polymorphic DNA element ispresent in at least one Methylobacterium strain selected from the groupconsisting of NLS0020, NLS0066, NLS0017, NLS0065, and NLS0089. Incertain embodiments, the composition is applied to a lettuce seed andthe Methylobacterium is selected from the group consisting of NLS0020,NLS0066, NLS0017, NLS0065, and NLS0089. In certain embodiments, thecomposition is applied to a lettuce plant or a part thereof and theleast one polymorphic DNA element is present in at least oneMethylobacterium strain selected from the group consisting of NLS0042,NLS0017, NLS0020, and NLS0068. In certain embodiments, the compositionis applied to a lettuce plant or a part thereof and the Methylobacteriumis selected from the group consisting of NLS0042, NLS0017, NLS0020, andNLS0068. In certain embodiments, the applied composition coats orpartially coats said plant or a part thereof, or said seed. In certainembodiments, the methods further comprise: (i) growing said lettuceplant or lettuce plant grown from said seed; and/or (ii) harvestingleaves or seed from said lettuce plant or lettuce plant grown from saidseed. In certain embodiments, the solid substance with adherentMethylobacterium is not a substance that promotes growth of residentmicroorganisms on the lettuce plant, the part thereof, or the lettuceseed. In certain embodiments, the composition comprises anagriculturally acceptable adjuvant and/or excipient. In certainembodiments of any of the aforementioned methods, the composition isdepleted of substances that promote growth of resident microorganisms onsaid plant or seed. Also provided are lettuce plant parts or lettuceseeds obtained by any of the aforementioned methods and that are coatedor partially coated with a composition comprising Methylobacterium.

Methods for improving lettuce plant production comprising applying acomposition comprising Methylobacterium to a lettuce plant, a partthereof, or lettuce seed, wherein said composition is depleted ofsubstances that promote growth of resident microorganisms on said plantor seed and wherein said plant or plant grown from said seed exhibits atrait improvement selected from the group consisting of an increasedrate of leaf growth, an increased rate of root growth, increased totalbiomass production, increased seed yield, decreased cycle time, andcombinations thereof when compared to an untreated control lettuce plantor a control lettuce plant grown from an untreated seed. In certainembodiments, the composition comprises a solid substance with adherentMethylobacterium grown thereon. In certain embodiments, the solidsubstance is not a substance that promotes growth of residentmicroorganisms on the lettuce plant, the part thereof, or the lettuceseed. In certain embodiments, the composition comprises Methylobacteriumat a titer of about 1×10⁶ CFU/gm to about 1×10¹¹ CFU/gm. In certainembodiments, the composition comprises a liquid, a solid substance withMethylobacterium adhered thereto in a liquid, a solid substance withMethylobacterium adhered thereto in an emulsion, or an emulsion. Incertain embodiments, the composition comprises Methylobacterium at atiter of about 1×10⁶ CFU/mL to about 1×10¹¹ CFU/mL. In certainembodiments, the methods further comprise: (i) growing said lettuceplant or lettuce plant grown from said seed; and/or (ii) harvestingleaves or seed from said lettuce plant or lettuce plant grown from saidseed. In certain embodiments, the Methylobacterium has at least one geneencoding at least one protein that is orthologous to a protein having anamino acid sequence of SEQ ID NO: 1-5125. In certain embodiments, theMethylobacterium has at least one gene encoding a protein that isorthologous to a reference protein of Table 7. In certain embodiments,the Methylobacterium sp. can contain at least one gene encoding aprotein that is orthologous to a reference protein having the amino acidsequence of 13, 14, 23, 27, 28, 30, 40, 43, 44, 51, 52, 57, 76, 85, 127,197, 198, 199, 1094, 1100, 1106, 1114,1116, 1117, 1120, 1180, 2180,2190, 2463, 2467, 2468, 2471, 2510, 2515, 2676, 2971, 3357, 3370, 3372,3394, 3427, 3429, 3430, 3950, 3952, 3968, 3987, 3996, 4004, 4006, and/or4067 of Table 7. In certain embodiments the Methylobacterium has atleast one gene encoding a protein that is orthologous to a referenceprotein is selected from the group consisting of SEQ ID NO: 13, 14, 23,1094, 1100, 1106, 2467, 2468, 3357, 3370, and/or 3968. In certainembodiments the Methylobacterium has at least one gene encoding aprotein that is orthologous to a reference protein is selected from thegroup consisting of SEQ ID NO: 1100, 1116, 2471 and/or 3950. In certainembodiments, the Methylobacterium in the composition or that is used isselected from the group consisting of NLS0017 (NRRL B-50931), NLS0020(NRRL B-50930), NLS0021 (NRRL B-50939), NLS0037 (NRRL B-50941), NLS0038(NRRL B-50942), NLS0042 (NRRL B-50932), NLS0046 (NRRL B-50929), NLS0062(NRRL B-50937), NLS0064 (NRRL B-50938), NLS0065 (NRRL B-50935), NLS0066(NRRL B-50940), NLS0068 (NRRL B-50934), NLS0069 (NRRL B-50936), NLS0089(NRRL B-50933), and derivatives thereof. In certain embodiments, theMethylobacterium in the composition or that is used is selected from thegroup consisting of NLS0017, NLS0037, NLS0066, NLS0020, NLS0042,NLS0065, NLS0089, NLS0046, NLS0021. NLS0069, NLS0068, NLS0064, NLS0062,NLS0038, and derivatives thereof. In certain embodiments the referenceprotein is selected from the group consisting of SEQ ID NO: 11000, 1116,2471 and/or 3950. In certain embodiments, the Methylobacterium has atleast one polymorphic DNA element that is present in at least oneMethylobacterium strain selected from the group consisting of NLS0020,NLS0066, NLS0017, NLS0065, NLS0089, NLS0042, and NLS0068 provided hereinthat improve lettuce production but that is absent from Methylobacteriumsp. that do not improve lettuce production. In certain embodiments, thecomposition is applied to a lettuce seed and the least one polymorphicDNA element is present in at least one Methylobacterium strain selectedfrom the group consisting of NLS0020, NLS0066, NLS0017, NLS0065, andNLS0089. In certain embodiments, the composition is applied to a lettuceseed and the Methylobacterium is selected from the group consisting ofNLS0020, NLS0066, NLS0017, NLS0065, and NLS0089. In certain embodiments,the composition is applied to a lettuce plant or a part thereof and theleast one polymorphic DNA element is present in at least oneMethylobacterium strain selected from the group consisting of NLS0042,NLS0017, NLS0020, and NLS0068. In certain embodiments, the compositionis applied to a lettuce plant or a part thereof and the Methylobacteriumis selected from the group consisting of NLS0042, NLS0017, NLS0020, andNLS0068. In certain embodiments of any of the aforementioned methods,the composition coats or partially coats said plant or a part thereof,or said seed. Also provided are lettuce plant parts or lettuce seedsobtained by any of the aforementioned methods and that are coated orpartially coated with a composition comprising Methylobacterium.

Compositions comprising: (i) a solid substance with adherentMethylobacterium grown thereon wherein said Methylobacterium has atleast one gene encoding a protein that is orthologous to a proteinhaving an amino acid sequence of SEQ ID NO: 1-5125;(ii) an emulsion withMethylobacterium grown therein wherein said Methylobacterium has atleast one gene encoding a protein that is orthologous to a proteinhaving an amino acid sequence of SEQ ID NO: 1-5125; or (iii) certainMethylobacterium strains selected from the group consisting of NLS0017(NRRL B-50931), NLS0020 (NRRL B-50930), NLS0021 (NRRL B-50939), NLS0037(NRRL B-50941), NLS0038 (NRRL B-50942), NLS0042 (NRRL B-50932), NLS0046(NRRL B-50929), NLS0062 (NRRL B-50937), NLS0064 (NRRL B-50938), NLS0065(NRRL B-50935), NLS0066 (NRRL B-50940), NLS0068 (NRRL B-50934), NLS0069(NRRL B-50936), NLS0089 (NRRL B-50933), and derivatives thereof and anagriculturally acceptable adjuvant, excipient, or combination thereofare provided herein. Also provided herein are compositions comprising:(a) (i) a solid substance with adherent Methylobacterium grown thereon;(ii) an emulsion with Methylobacterium grown therein; or (iii) aMethylobacterium that has at least one gene encoding a protein that isorthologous to a protein having an amino acid sequence of SEQ ID NO:1-5125; and (b) an agriculturally acceptable excipient, adjuvant, orcombination thereof. In certain embodiments, the Methylobacterium has atleast one gene encoding a protein that is orthologous to a referenceprotein of Table 7. In certain embodiments, the reference protein isselected from the group consisting of SEQ ID NO: 13, 14, 23, 1094, 1100,1106, 2467, 2468, 3357, 3370, and/or 3968. In certain embodiments, theMethylobacterium is selected from the group consisting of NLS0017 (NRRLB-50931), NLS0020 (NRRL B-50930), NLS0037 (NRRL B-50941), NLS0042 (NRRLB-50932), NLS0065 (NRRL B-50935), NLS0066 (NRRL B-50940), andderivatives thereof. Also provided are compositions comprising: (i) asolid substance with adherent Methylobacterium grown thereon; or (ii) anemulsion with Methylobacterium grown therein, wherein saidMethylobacterium has at least one polymorphic DNA element that ispresent in at least one Methylobacterium strain selected from the groupconsisting of NLS0020, NLS0066, NLS0017, NLS0065, NLS0089, NLS0042, andNLS0068 provided herein that improve lettuce production but that isabsent from Methylobacterium sp. that do not improve lettuce production.In certain embodiments, the at least one polymorphic DNA element ispresent in at least one Methylobacterium strain selected from the groupconsisting of NLS0020, NLS0066, NLS0017, NLS0065, and NLS0089. Incertain embodiments, the least one polymorphic DNA element is present inat least one Methylobacterium strain selected from the group consistingof NLS0042, NLS0017, NLS0020, and NLS0068. In certain embodiments, theMethylobacterium is selected from the group consisting of NLS0020,NLS0066, NLS0017, NLS0065, NLS0089, NLS0042, and NLS0068. In certainembodiments, the composition is depleted of substances that promotegrowth of resident microorganisms on a plant or seed. In certainembodiments, the substance that promotes growth of residentmicroorganisms on a plant or seed is selected from the group consistingof a carbon source, a nitrogen source, a phosphorous source, a sulfursource, a magnesium source, and combinations thereof. In certainembodiments, the compositions further comprise an agriculturallyacceptable adjuvant and/or excipient. In certain embodiments, the solidsubstance with adherent Methylobacterium grown thereon has aMethylobacterium titer of at least about 5×10⁸ CFU/gm to at least about1×10¹¹ CFU/gm. In certain embodiments, the Methylobacterium is selectedfrom the group consisting of NLS0020, NLS0066, NLS0017, NLS0065, andNLS0089. In certain embodiments, the aforementioned compositions areadapted for use in treating a plant or seed or is used to treat a plantor seed. Also provided herein is a lettuce plant part or lettuce seedthat is coated or partially coated with any of the aforementioned thecompositions. In certain embodiments, the coated or partially coatedlettuce plant part or lettuce seed is obtained by any of theaforementioned methods.

Also provided is an isolated Methylobacterium selected from the groupconsisting of NLS0017 (NRRL B-50931), NLS0020 (NRRL B-50930), NLS0021(NRRL B-50939), NLS0037 (NRRL B-50941), NLS0038 (NRRL B-50942), NLS0042(NRRL B-50932), NLS0046 (NRRL B-50929), NLS0062 (NRRL B-50937), NLS0064(NRRL B-50938), NLS0065 (NRRL B-50935), NLS0066 (NRRL B-50940), NLS0068(NRRL B-50934), NLS0069 (NRRL B-50936), NLS0089 (NRRL B-50933), andderivatives thereof.

Also provided are compositions comprising: (i) an isolatedMethylobacterium selected from the group consisting of NLS0017 (NRRLB-50931), NLS0020 (NRRL B-50930), NLS0021 (NRRL B-50939), NLS0037 (NRRLB-50941), NLS0038 (NRRL B-50942), NLS0042 (NRRL B-50932), NLS0046 (NRRLB-50929), NLS0062 (NRRL B-50937), NLS0064 (NRRL B-50938), NLS0065 (NRRLB-50935), NLS0066 (NRRL B-50940), NLS0068 (NRRL B-50934), NLS0069 (NRRLB-50936), NLS0089 (NRRL B-50933), derivatives thereof; and (ii) anagriculturally acceptable adjuvant, excipient, or combination thereof.

Also provided are plants, plant parts, and plant seeds that are coatedor partially coated with any of the aforementioned compositions. Incertain embodiments, a lettuce plant, plant part, or plant seed iscoated or partially coated with the aforementioned compositions.

Also provided herein are methods of identifying compositions, plantparts, plant seeds, or processed plant products comprisingMethylobacterium sp. NLS0017 (NRRL B-50931), NLS0020 (NRRL B-50930),NLS0037 (NRRL B-50941), NLS0042 (NRRL B-50932), NLS0065 (NRRL B-50935),or NLS0066 (NRRL B-50940) by assaying for the presence of nucleic acidsequences contained in SEQ ID NO: 5126-10250 in those materials. Incertain embodiments, such methods can comprise subjecting a samplesuspected of containing Methylobacterium sp. NLS0017 (NRRL B-50931),NLS0020 (NRRL B-50930), NLS0037 (NRRL B-50941), NLS0042 (NRRL B-50932),NLS0065 (NRRL B-50935), or NLS0066 (NRRL B-50940) to a nucleic acidanalysis technique and determining that the sample contains one or morenucleic acid containing a sequence of at least about 20, 50, 100, 200,500, or a 1000 nucleotides that is identical to at least one of SEQ IDNO: 5126-10250, wherein the presence of a sequence that is identical toat least one of SEQ ID NO: 5126-6211 is indicative of the presence ofNLS017, wherein the presence of a sequence that is identical to at leastone of SEQ ID NO: 6212-7301 is indicative of the presence of NLS020,wherein the presence of a sequence that is identical to at least one ofSEQ ID NO: 7302-7586 is indicative of the presence of NLS037, whereinthe presence of a sequence that is identical to at least one of SEQ IDNO: 7587-8472 is indicative of the presence of NLS042, wherein thepresence of a sequence that is identical to at least one of SEQ ID NO:8473-9074 is indicative of the presence of NLS065, and wherein thepresence of a sequence that is identical to at least one of SEQ ID NO:9075-10250 is indicative of the presence of NLS066. Such nucleic acidanalyses include, but are not limited to, techniques based on nucleicacid hybridization, polymerase chain reactions, mass spectroscopy,nanopore based detection, branched DNA analyses, combinations thereof,and the like.

Also provided herein are methods of identifying Methylobacterium sp.that can confer useful traits to plants by assaying for the presence ofnucleic acid sequences contained in SEQ ID NO: 5126-10250 in theMethylobacterium sp. In certain embodiments, such methods can comprisesubjecting a candidate Methylobacterium sp. to a nucleic acid analysistechnique and determining that the sample contains one or more nucleicacid containing a sequence of at least about 20, 50, 100, 200, 500, or a1000 nucleotides that is identical to at least one of SEQ ID NO:5126-10250 indicates that the candidate Methylobacterium sp. that canconfer a useful traits to a plant. Such nucleic acid analyses include,but are not limited to, techniques based on nucleic acid hybridization,polymerase chain reactions, mass spectroscopy, nanopore based detection,branched DNA analyses, combinations thereof, and the like.

DESCRIPTION Definitions

As used herein, the phrases “adhered thereto” and “adherent” refer toMethylobacterium that are associated with a solid substance by growing,or having been grown, on a solid substance.

As used herein, the phrase “agriculturally acceptable adjuvant” refersto a substance that enhances the performance of an active agent in acomposition for treatment of plants and/or plant parts. In certaincompositions, an active agent can comprise a mono-culture or co-cultureof Methylobacterium.

As used herein, the phrase “agriculturally acceptable excipient” refersto an essentially inert substance that can be used as a diluent and/orcarrier for an active agent in a composition for treatment of plantsand/or plant parts. In certain compositions, an active agent cancomprise a mono-culture or co-culture of Methylobacterium.

As used herein, the term “Methylobacterium” refers to bacteria that arefacultative methylotrophs of the genus Methylobacterium. The termMethylobacterium, as used herein, thus does not encompass includesspecies in the genera Methylobacter, Methylomonas, Methylomicrobium,Methylococcus, Methylosinus, Methylocystis, Methylosphaera,Methylocaldum, and Methylocella, which are obligate methanotrophs.

As used herein, the phrase “co-culture of Methylobacterium” refers to aMethylobacterium culture comprising at least two strains ofMethylobacterium or at least two species of Methylobacterium.

As used herein, the phrase “contaminating microorganism” refers tomicroorganisms in a culture, fermentation broth, fermentation brothproduct, or composition that were not identified prior to introductioninto the culture, fermentation broth, fermentation broth product, orcomposition.

As used herein, the phrase “derivatives thereof”, when used in thecontext of a Methylobacterium isolate, refers to any strain that isobtained from the Methylobacterium isolate. Derivatives of aMethylobacterium isolate include, but are not limited to, variants ofthe strain obtained by selection, variants of the strain selected bymutagenesis and selection, and a genetically transformed strain obtainedfrom the Methylobacterium isolate.

As used herein, the term “emulsion” refers to a colloidal mixture of twoimmiscible liquids wherein one liquid is the continuous phase and theother liquid is the dispersed phase. In certain embodiments, thecontinuous phase is an aqueous liquid and the dispersed phase is liquidthat is not miscible, or partially miscible, in the aqueous liquid.

As used herein, the phrase “essentially free of contaminatingmicroorganisms” refers to a culture, fermentation broth, fermentationproduct, or composition where at least about 95% of the microorganismspresent by amount or type in the culture, fermentation broth,fermentation product, or composition are the desired Methylobacterium orother desired microorganisms of pre-determined identity.

As used herein, the phrase “inanimate solid substance” refers to asubstance which is insoluble or partially soluble in water or aqueoussolutions and which is either non-living or which is not a part of astill-living organism from which it was derived.

As used herein, the phrase “mono-culture of Methylobacterium” refers toa Methylobacterium culture consisting of a single strain ofMethylobacterium.

As used herein, the term “peptide” refers to any polypeptide of 50 aminoacid residues or less.

As used herein, the term “lettuce” refers to Lactuca sp. plants. Lactucasp. plants include, but are not limited to, Lactuca biennis, Lactucacanadensis, Lactuca floridana, Lactuca graminifolia, Lactuca hirsuta,Lactuca indica, Lactuca ludoviciana, Lactuca saligna, Lactuca sativa,Lactuca serriola, Lactuca terrae-novae, Lactuca virosa, andLactuca×morssii species.

As used herein, the term “protein” refers to any polypeptide having 51or more amino acid residues.

As used herein, a “pesticide” refers to an agent that is insecticidal,fungicidal, nematocidal, bacteriocidal, or any combination thereof.

As used herein, the phrase “bacteriostatic agent” refers to agents thatinhibit growth of bacteria but do not kill the bacteria.

As used herein, the phrase “pesticide does not substantially inhibitgrowth of said Methylobacterium” refers to any pesticide that whenprovided in a composition comprising a fermentation product comprising asolid substance wherein a mono-culture or co-culture of Methylobacteriumis adhered thereto, results in no more than a 50% inhibition ofMethylobacterium growth when the composition is applied to a plant orplant part in comparison to a composition lacking the pesticide. Incertain embodiments, the pesticide results in no more than a 40%, 20%,10%, 5%, or 1% inhibition of Methylobacterium growth when thecomposition is applied to a plant or plant part in comparison to acomposition lacking the pesticide.

As used herein, the term “PPFM bacteria” refers without limitation tobacterial species in the genus Methylobacterium other than M nodulans.

As used herein, the phrase “solid substance” refers to a substance whichis insoluble or partially soluble in water or aqueous solutions.

As used herein, the phrase “solid phase that can be suspended therein”refers to a solid substance that can be distributed throughout a liquidby agitation.

As used herein, the term “non-regenerable” refers to either a plant partor processed plant product that cannot be regenerated into a wholeplant.

As used herein, the phrase “substantially all of the solid phase issuspended in the liquid phase” refers to media wherein at least 95%,98%, or 99% of solid substance(s) comprising the solid phase aredistributed throughout the liquid by agitation.

As used herein, the phrase “substantially all of the solid phase is notsuspended in the liquid phase” refers to media where less than 5%, 2%,or 1% of the solid is in a particulate form that is distributedthroughout the media by agitation.

As used herein, the phrase “resident microorganism” refers to residentbacteria, fungi or yeast.

As used herein, the phrase “substance that promotes growth of residentmicroorganisms on a plant or seed” refers to a carbon source, a nitrogensource, a phosphorous source, and combinations thereof.

To the extent to which any of the preceding definitions is inconsistentwith definitions provided in any patent or non-patent referenceincorporated herein by reference, any patent or non-patent referencecited herein, or in any patent or non-patent reference found elsewhere,it is understood that the preceding definition will be used herein.

Methylobacterium-Containing Compositions Depleted of Substances thatPromote Growth of Resident Bacteria on a Plant or Seed, Methods of theirUse, and Methods of Making

Compositions comprising Methylobacterium that are depleted of substancesthat promote growth of resident bacteria on a plant or seed, methods ofusing the compositions to improve lettuce production, and methods ofmaking the compositions are provided herein. In certain embodiments ofany of the aforementioned compositions, the composition comprises asolid substance wherein a mono-culture or co-culture of Methylobacteriumis adhered thereto. In certain embodiments where the Methylobacterium isadhered to a solid substance, the composition comprises a colloid formedby the solid substance wherein a mono-culture or co-culture ofMethylobacterium is adhered thereto and a liquid. In certainembodiments, the colloid is a gel. In certain embodiments of certainaforementioned compositions, composition is an emulsion that does notcontain a solid substance.

Compositions that comprise a solid substance with adherentMethylobacterium grown thereon is provided. In certain embodiments, theadherent Methylobacterium can be at a titer of at least about 5×10⁸CFU/gm to at least about 5×10¹³ CFU/gm or about 1×10¹⁴ CFU/gm and thecomposition is depleted of substances that promote growth of residentmicroorganisms on a plant or seed.

In certain embodiments, the compositions containing Methylobacteriumprovided or used herein are depleted of substances that promote growthof the resident microorganisms when one or more of those substances areabsent or are essentially absent. In certain embodiments, thecomposition is depleted of substances that promote growth of theresident microorganisms when those substances are present at apercentage of no more than about 5%, 2%, 1%, 0.5%, 0.2%, or 0.1% of thetotal mass, mass/total volume, or total volume of the composition. Incertain embodiments, substance that promotes growth of residentmicroorganisms on a plant or seed is selected from the group consistingof a carbon source, a nitrogen source, a phosphorous source, a sulfursource, a magnesium source, and combinations thereof. Carbon sourcesinclude, but are not limited to, alcohols, monosaccharides,disaccharides, polysaccharides, lipids, fatty acids, and the like.Alcohols that are depleted include, but are not limited to, methanol,ethanol, glycerol, and the like. Nitrogen sources include, but are notlimited to, ammonia and various compounds containing amino groups thatcan be metabolized by microorganisms. In certain embodiments, thesubstance that is depleted is a source of two or more of a carbonsource, a nitrogen source, a phosphorous source, a sulfur source, and amagnesium source. For example, the composition that is depleted of aminoacids or peptides and lacks other carbon or nitrogen sources is depletedfor both a carbon and a nitrogen source. In certain embodiments, thecomposition comprises an agriculturally acceptable adjuvant and/orexcipient.

Resident microorganisms on the plant or seed include, but are notlimited to bacteria, fungi, and yeast. Substances that promote thegrowth of such microorganisms can be identified by methods including,but not limited to, assaying the plant or seed surface for the amount ornumber of microorganisms present prior to exposure of the plant or seedto the substance (or to a composition containing the substance),exposing the assayed plant or seed to the substance or composition inparallel with a control composition lacking the substance, and thenre-assaying the plant or seed surface for the amount or number ofmicroorganisms present after a suitable time interval and under suitableconditions of temperature to allow growth of the residentmicroorganisms. Assays for numbers of microorganisms include, but arenot limited to, determinations of colony forming units per an amount ofplant or seed exposed to the substance and the control.

Without seeking to be limited by theory, it is believed that thecompositions containing Methylobacterium provided or used herein thatare depleted of substances that promote growth of the residentmicroorganisms can result in superior results in comparison to othercompositions containing such substances when applied to plants, plantparts, or seeds. Such superior results are believed to include, but arenot limited to, improved plant yield, pathogen resistance, insectresistance, fruit ripening and the like. While not seeking to be limitedby theory, it is believed that the compositions containingMethylobacterium that are depleted of substances that promote growth ofthe resident microorganisms allow for more efficient and or extensivecolonization of the plant, part thereof, or seed as competition for oneor more of space or nutrients by the resident microorganisms is reduced.

Also provided herein are methods for improving lettuce production thatcomprise applying any of the aforementioned compositions orMethylobacterium provided herein to a lettuce plant, lettuce plant part,or lettuce seed, and, optionally, growing the plant and/or harvestingleaves or seed from the plant or a plant grown from the seed. In certainembodiments, the composition coats or partially coats the lettuce plant,plant part, or seed. The treated lettuce plant or plant grown from theseed exhibits an increased rate of root growth, an increased rate ofleaf growth, increased seed production, a decreased cycle time (fromseed planting to seed production) and/or increased total biomasscompared to an untreated control lettuce plant or control lettuce plantgrown from untreated seed, thereby obtaining improved lettuceproduction. In certain embodiments, application of the compositionprovides for at least about a 5%, 10%, 15%, 20%, 30% or 40% increase inroot growth rate, leaf growth rate, seed production, and/or increasedtotal biomass in the lettuce plant, lettuce plant part, or a lettuceplant derived therefrom in comparison to an untreated control lettuceplant or control lettuce plant grown from an untreated seed. In certainembodiments, application of the composition provides for about a 5% or10% to about a 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 60%, or 70%increase in root growth rate, leaf growth rate, seed production, and/orincreased total biomass in the plant, plant part, or a plant derivedtherefrom in comparison to an untreated control lettuce plant or controllettuce plant grown from an untreated seed. In certain embodiments,application of the composition provides for at least about a 5%, 10%,15%, 20%, 30% or 40% decrease in cycle time in the treated lettuce plantor a lettuce plant grown from a treated seed in comparison to theuntreated control lettuce plant or control lettuce plant grown from anun-treated seed. In certain embodiments, application of the compositionprovides for about a 5% or 10% to about a 15%, 20%, 25%, 30%, 35%, 40%,45%, or 50% decrease in cycle time in the treated lettuce plant or alettuce plant grown from a treated seed in comparison to an untreatedcontrol lettuce plant or control lettuce plant grown from an untreatedseed. In certain embodiments, the lettuce plant part is a leaf, a stem,a flower, a root, a tuber, or a seed. In certain embodiments, the methodfurther comprises the steps of growing the plant and/or the step ofharvesting at least one plant part selected from the group consisting ofa leaf, a stem, a flower, a root, a tuber, or a seed from the lettuceplant or plant part. In certain embodiments of any of the aforementionedmethods, the methods further comprise obtaining a processed food or feedcomposition from the plant or plant part. In certain embodiments, theprocessed food composition comprises chopped or cut lettuce leaves.

Also provided are methods of making a lettuce plant or plant seedtreatment composition that comprises Methylobacterium and is depleted ofsubstances that promote growth of resident bacteria on a plant or seedis provided herein. Such method comprises (i) growing a mono-culture orco-culture of Methylobacterium in media that comprises an aqueous phase,a liquid phase and a solid phase, or an emulsion, thereby obtaining aMethylobacterium-containing media; (ii) separating the Methylobacteriumfrom at least one other portion of the Methylobacterium-containingmedia; and (iii) reconstituting the Methylobacterium in a matrix lackingsubstances that promote growth of resident bacteria on a plant or seed.In certain embodiments, the separation step is effected bycentrifugation, filtration, or settling of theMethylobacterium-containing media and removal of excess liquid oremulsion therefrom. In certain embodiments, the substance that promotesgrowth of resident bacteria on a plant or seed is selected from thegroup consisting of a carbon source, a nitrogen source, a phosphoroussource, and combinations thereof. In certain embodiments, the matrix isa liquid, an emulsion, or one or more solids, and comprises anagriculturally acceptable adjuvant and/or excipient. Still in certainembodiments; the Methylobacterium are grown in media comprising a liquidphase and a solid substance with adherent Methylobacterium grownthereon. The solid substance is separated from the liquid phase of theMethylobacterium-containing media, and the solid substance with adherentMethylobacterium grown thereon is reconstituted in the aforementionedmatrix. In certain embodiments of the methods, the Methylobacterium sp.,is selected from the group consisting of M. aminovorans, M. extorquens,M. fujisawaense, M. mesophilicum, M. radiotolerans, M. rhodesianum, M.nodulans, M. phyllosphaerae, M. thiocyanatum, and M. oryzae. In certainembodiments of the methods, the Methylobacterium is not M. radiotoleransor M. oryzae. In certain embodiments of the methods, theMethylobacterium is adhered to a solid substance. In certain embodimentsof the methods, the Methylobacterium is adhered to the solid substanceis combined with a liquid to form a composition that is a colloid. Incertain embodiments of the methods, the colloid is a gel. In certainembodiments of the methods, the Methylobacterium adhered to the solidsubstance is provided by culturing the Methylobacterium in the presenceof the solid substance. In certain embodiments of the methods, thecomposition comprises an emulsion. In certain embodiments of themethods, the Methylobacterium is provided by culturing theMethylobacterium in an emulsion.

Methods where Methylobacterium are cultured in biphasic media comprisinga liquid phase and a solid substance have been found to significantlyincrease the resultant yield of Methylobacterium relative to methodswhere the Methylobacterium are cultured in liquid media alone. Incertain embodiments, the methods can comprise growing theMethylobacterium in liquid media with a particulate solid substance thatcan be suspended in the liquid by agitation under conditions thatprovide for Methylobacterium growth. In certain embodiments whereparticulate solid substances are used, at least substantially all of thesolid phase can thus be suspended in the liquid phase upon agitation.Such particulate solid substances can comprise materials that are about1 millimeter or less in length or diameter. In certain embodiments, thedegree of agitation is sufficient to provide for uniform distribution ofthe particulate solid substance in the liquid phase and/or optimallevels of culture aeration. However, in other embodiments providedherein, at least substantially all of the solid phase is not suspendedin the liquid phase, or portions of the solid phase are suspended in theliquid phase and portions of the solid phase are not suspended in theliquid phase. Non-particulate solid substances can be used in certainbiphasic media where the solid phase is not suspended in the liquidphase. Such non-particulate solid substances include, but are notlimited to, materials that are greater than about 1 millimeter in lengthor diameter. Such particulate and non-particulate solid substances alsoinclude, but are not limited to, materials that are porous, fibrous, orotherwise configured to provide for increased surface areas for adherentgrowth of the Methylobacterium. Biphasic media where portions of thesolid phase are suspended in the liquid phase and portions of the solidphase are not suspended in the liquid phase can comprise a mixture ofparticulate and non-particulate solid substances. Such particulate andnon-particulate solid substances used in any of the aforementionedbiphasic media also include, but are not limited to, materials that areporous, fibrous, or otherwise configured to provide for increasedsurface areas for adherent growth of the Methylobacterium. In certainembodiments, the media comprises a colloid formed by a solid and aliquid phase. A colloid comprising a solid and a liquid can bepre-formed and added to liquid media or can be formed in mediacontaining a solid and a liquid. Colloids comprising a solid and aliquid can be formed by subjecting certain solid substances to achemical and/or thermal change. In certain embodiments, the colloid is agel. In certain embodiments, the liquid phase of the media is anemulsion. In certain embodiments, the emulsion comprises an aqueousliquid and a liquid that is not miscible, or only partially miscible, inthe aqueous liquid. Liquids that are not miscible, or only partiallymiscible, in water include, but are not limited to, any of thefollowing: (1) liquids having a miscibility in water that is equal to orless than that of pentanol, hexanol, or heptanol at 25 degrees C.; (2)liquids comprising an alcohol, an aldehyde, a ketone, a fatty acid, aphospholipid, or any combination thereof; (3) alcohols selected from thegroup consisting of aliphatic alcohols containing at least 5 carbons andsterols; (4) an animal oil, microbial oil, synthetic oil, plant oil, orcombination thereof; and/or, (5) a plant oil is selected from the groupconsisting of corn, soybean, cotton, peanut, sunflower, olive, flax,coconut, palm, rapeseed, sesame seed, safflower, and combinationsthereof. In certain embodiments, the immiscible or partially immiscibleliquid can comprises at least about 0.02% to about 20% of the liquidphase by mass. In certain embodiments, the methods can compriseobtaining a biphasic culture media comprising the liquid, the solid, andMethylobacterium and incubating the culture under conditions thatprovide for growth of the Methylobacterium. Biphasic culture mediascomprising the liquid, the solid, and Methylobacterium can be obtainedby a variety of methods that include, but are not limited to, any of:(a) inoculating a biphasic media comprising the liquid and the solidsubstance with Methylobacterium; (b) inoculating the solid substancewith Methylobacterium and then introducing the solid substancecomprising the Methylobacterium into the liquid media; (c) inoculatingthe solid substance with Methylobacterium, incubating theMethylobacterium on the solid substance, and then introducing the solidsubstance comprising the Methylobacterium into the liquid media; or (d)any combination of (a), (b), or (c). Methods and compositions forgrowing Methylobacterium in biphasic media comprising a liquid and asolid are disclosed in co-assigned U.S. patent application Ser. No.13/907,161, filed May 31, 2013, which is incorporated herein byreference in its entirety, and in co-assigned International PatentApplication PCT/US13/43722, filed May 31, 2013, which is incorporatedherein by reference in its entirety.

Methods where Methylobacterium are cultured in media comprising anemulsion have also been found to significantly increase the resultantyield of Methylobacterium relative to methods where the Methylobacteriumare cultured in liquid media alone. In certain embodiments, the methodsfor making the compositions provided herein can comprise growing theMethylobacterium agent in an emulsion under conditions that provide forMethylobacterium growth. Medias comprising the emulsion andMethylobacterium can be obtained by a variety of methods that include,but are not limited to, any of: (a) inoculating a media comprising theemulsion with Methylobacterium; (b) inoculating the aqueous liquid withthe Methylobacterium, introducing the non-aqueous liquid, and mixing toform an emulsion; (c) inoculating the aqueous liquid with theMethylobacterium, introducing the non-aqueous liquid, and mixing to forman emulsion; or (d) any combination of (a), (b), or (c). In certainembodiments, the emulsion comprises an aqueous liquid and a liquid thatis not miscible, or only partially miscible, in the aqueous liquid.Non-aqueous liquids that are not miscible, or only partially miscible,in water include, but are not limited to, any of the following: (1)liquids having a miscibility in water that is equal to or less than thatof n-pentanol, n-hexanol, or n-heptanol at 25 degrees C.; (2) liquidscomprising an alcohol, an aldehyde, a ketone, a fatty acid, aphospholipid, or any combination thereof; (3) alcohols is selected fromthe group consisting of aliphatic alcohols containing at least 5, 6, or7 carbons and sterols; (4) an animal oil, microbial oil, synthetic oil,plant oil, or combination thereof; and/or, (5) a plant oil is selectedfrom the group consisting of corn, soybean, cotton, peanut, sunflower,olive, flax, coconut, palm, rapeseed, sesame seed, safflower, andcombinations thereof. In certain embodiments, the immiscible orpartially immiscible non-aqueous liquid can comprise at least about0.02% to about 20% of the emulsion by mass. In certain embodiments, theimmiscible or partially immiscible non-aqueous liquid can comprise atleast about any of about 0.05%, 0.1%, 0.5%, or 1% to about 3%, 5%, 10%,or 20% of the emulsion by mass. Methods and compositions for growingMethylobacterium in media comprising an emulsion are disclosed inco-assigned International Patent Application PCT/US2014/040218, filedMay 30, 2014, which is incorporated herein by reference in its entirety.

In certain embodiments, the fermentation broth, fermentation brothproduct, or compositions that comprise Methylobacterium sp. can furthercomprise one or more introduced microorganisms of pre-determinedidentity other than Methylobacterium. Other microorganisms that can beadded include, but are not limited to, microorganisms that arebiopesticidal or provide some other benefit when applied to a plant orplant part. Biopesticidal or otherwise beneficial microorganisms thusinclude, but are not limited to, various Bacillus sp., Pseudomonas sp.,Coniothyrium sp., Pantoea sp., Streptomyces sp., and Trichoderma sp.Microbial biopesticides can be a bacterium, fungus, virus, or protozoan.Particularly useful biopesticidal microorganisms include variousBacillus subtilis, Bacillus thuringiensis, Bacillus pumilis, Pseudomonassyringae, Trichoderma harzianum, Trichoderma vixens, and Streptomyceslydicus strains. Other microorganisms that are added can be geneticallyengineered or naturally occurring isolates that are available as purecultures. In certain embodiments, it is anticipated that the bacterialor fungal microorganism can be provided in the fermentation broth,fermentation broth product, or composition in the form of a spore.

In certain embodiments, the liquid culture medium is prepared frominexpensive and readily available components, including, but not limitedto, inorganic salts such as potassium phosphate, magnesium sulfate andthe like, carbon sources such as glycerol, methanol, glutamic acid,aspartic acid, succinic acid and the like, and amino acid blends such aspeptone, tryptone, and the like. Exemplary liquid media that can be usedinclude, but are not limited to, ammonium mineral salts (AMS) medium(Whittenbury et al., 1970), Vogel-Bonner (VB) minimal culture medium(Vogel and Bonner, 1956), and LB broth (“Luria-Bertani Broth”).

In general, the solid substance used in the methods and compositionsthat provide for the efficient growth of Methylobacterium can be anysuitable solid substance which is insoluble or only partially soluble inwater or aqueous solutions. Such suitable solid substances are alsonon-bacteriocidal or non-bacteriostatic with respect to Methylobacteriumwhen the solid substances are provided in the liquid culture media. Incertain embodiments, such suitable solid substances are also solidsubstances that are readily obtained in sterile form or renderedsterile. Solid substances used herein can be sterilized by any methodthat provides for removal of contaminating microorganisms and thusinclude, but are not limited to, methods such as autoclaving,irradiation, chemical treatment, and any combination thereof. Thesesolid substances include natural substances of animal, plant, microbial,fungal, or mineral origin, manmade substances, or combinations ofnatural and manmade substances. In certain embodiments, the solidsubstances are inanimate solid substances. Inanimate solid substances ofanimal, plant, microbial, or fungal origin can be obtained from animals,plants, microbes, or fungi that are unviable (i.e. no longer living) orthat have been rendered unviable. Diatom shells are thus inanimate solidsubstances when previously associated diatom algae have been removed orotherwise rendered inviable. Since diatom shells are inanimate solidsubstances, they are not considered to be photosynthetic organisms orphotosynthetic microorganisms. In certain embodiments, solid substancesinclude, but are not limited to, sand, silt, soil, clay, ash, charcoal,diatomaceous earth and other similar minerals, ground glass or glassbeads, ground ceramic materials, ceramic beads, bentonite, kaolin, talc,perlite, mica, vermiculite, silicas, quartz powder, montmorillonite, andcombinations thereof. In certain embodiments, the solid substance can bea polymer or polymeric beads. Polymers that can be used as a solidsubstance include, but are not limited to, various polysaccharides suchas cellulosic polymers and chitinous polymers which are insoluble oronly partially soluble in water or aqueous solutions, agar (i.e.galactans), and combinations thereof. In certain embodiments, the solidsubstance can be an insoluble or only partially soluble salt crystal.Salt crystals that can be used include, but are not limited to,insoluble or only partially soluble carbonates, chromates, sulfites,phosphates, hydroxides, oxides, and sulfides. In certain embodiments,the solid substance can be a microbial cell, fungal cell, microbialspore, or fungal spore. In certain embodiments, the solid substance canbe a microbial cell or microbial spore wherein the microbial cell ormicrobial spore is not a photosynthetic microorganism. In certainembodiments, the microbial cell or microbial spore is not aphotosynthetic microorganism, where the photosynthetic microorganism isselected from the group consisting of algae, cyanobacteria, diatoms,Botryococcus braunii, Chlorella, Dunaliella tertiolecta, Gracilaria,Pleurochrysis carterae, Sargassum, and Ulva. In still other embodiments,the solid substance can be an inactivated (i.e., unviable) microbialcell, fungal cell, microbial spore, or fungal spore. In still otherembodiments, the solid substance can be a quiescent (i.e. viable but notactively dividing) microbial cell, fungal cell, microbial spore, orfungal spore. In still other embodiments, the solid substance can becellular debris of microbial origin. In still other embodiments, thesolid substance can be particulate matter from any part of a plant.Plant parts that can be used to obtain the solid substance include, butare not limited to, cobs, husks, hulls, leaves, roots, flowers, stems,barks, seeds, and combinations thereof. Products obtained from processedplant parts including, but not limited to, bagasse, wheat bran, soygrits, crushed seed cake, stover, and the like can also be used. Suchplant parts, processed plants, and/or processed plant parts can bemilled to obtain the solid material in a particulate form that can beused. In certain embodiments, wood or a wood product including, but notlimited to, wood pulp, sawdust, shavings, and the like can be used. Incertain embodiments, the solid substance can be a particulate matterfrom an animal(s), including, but not limited to, bone meal, gelatin,ground or powdered shells, hair, macerated hide, and the like.

In certain embodiments, the solid substance is provided in a particulateform that provides for distribution of the solid substance in theculture media. In certain embodiments, the solid substance is comprisedof particle of about 2 microns to about 1000 microns in average lengthor average diameter. In certain embodiments, the solid substance iscomprised of particle of about 1 microns to about 1000 microns inaverage length or average diameter. In certain embodiments, the solidsubstance is a particle of about 1, 2, 4, 10, 20, or 40 microns to anyof about 100, 200, 500, 750, or 1000 microns in average length oraverage diameter. Desirable characteristics of particles used in themethods and compositions provided herein include suitable wettabilitysuch that the particles can be suspended throughout the media uponagitation.

In certain embodiments, the solid substance is provided in the media asa colloid wherein the continuous phase is a liquid and the dispersedphase is the solid. Suitable solids that can be used to form colloids inliquid media used to grow Methylobacterium include, but are not limitedto, various solids that are referred to as hydrocolloids. Suchhydrocolloids used in the media, methods and compositions providedherein can be hydrophilic polymers, of plant, animal, microbial, orsynthetic origin. Hydrocolloid polymers used in the methods can containmany hydroxyl groups and/or can be polyelectrolytes. Hydrocolloidpolymers used in the compositions and methods provided herein include,but are not limited to, agar, alginate, arabinoxylan, carrageenan,carboxymethylcellulose, cellulose, curdlan, gelatin, gellan, β-glucan,guar gum, gum arabic, locust bean gum, pectin, starch, xanthan gum, andmixtures thereof. In certain embodiments, the colloid used in the media,methods, and compositions provided herein can comprise a hydrocolloidpolymer and one or more proteins.

In certain embodiments, the solid substance can be a solid substancethat provides for adherent growth of Methylobacterium on the solidsubstance. Methylobacterium that are adhered to a solid substance areMethylobacterium that cannot be substantially removed by simply washingthe solid substance with the adherent Methylobacterium with growth mediawhereas non-adherent Methylobacterium can be substantially removed bywashing the solid substance with liquid growth media. In this context,“substantially removed” means that at least about 30%, 40%, 50%, 60%,70%, or 80% the Methylobacterium present are removed when the solidsubstance is washed with three volumes of liquid growth media. Suchwashing can be effected by a variety of methods including, but notlimited to, decanting liquid from a washed solid phase or passing liquidthrough a solid phase on a filter that permits flow through of bacteriain the liquid. In certain embodiments, the adherent Methylobacteriumthat are associated with the solid can include both Methylobacteriumthat are directly attached to the solid and/or Methylobacterium that areindirectly attached to the solid substance. Methylobacterium that areindirectly attached to the solid substance include, but are not limitedto, Methylobacterium that are attached to another Methylobacterium or toanother microorganism that is attached to the solid substance,Methylobacterium that are attached to the solid substance by beingattached to another substance that is attached to the solid substance,and the like. In certain embodiments, at least 10%, 20%, 30%, 40%, 50%,60%, 70%, 80%, 90%, 95%, 98%, 99%, 99.5% or 99.9% of theMethylobacterium in the fermentation broth, fermentation broth product,or compositions are Methylobacterium that are adhered to the solidsubstance. In certain embodiments, adherent Methylobacterium can bepresent on the surface of the solid substance in the fermentation broth,fermentation broth product, or composition at a density of at leastabout 1 Methylobacterium/20 square micrometers, of at least about 1Methylobacterium/10 square micrometers, of at least about 1Methylobacterium/10 square micrometers, of at least about 1Methylobacterium/5 square micrometers, of at least about 1Methylobacterium/2 square micrometers, or of at least about 1Methylobacterium/square micrometer. In certain embodiments, adherentMethylobacterium can be present on the surface of the solid substance inthe fermentation broth, fermentation broth product, or composition at adensity of at least about 1 Methylobacterium/20 square micrometers toabout 1 Methylobacterium/square micrometer, of at least about 1Methylobacterium/10 square micrometers to about 1Methylobacterium/square micrometer, of at least about 1Methylobacterium/10 square micrometers to about 1Methylobacterium/square micrometer, of at least about 1Methylobacterium/5 square micrometers to about 1 Methylobacterium/squaremicrometer, or of at least about 1 Methylobacterium/2 square micrometersto about 1 Methylobacterium/square micrometer. In certain embodiments,adherent Methylobacterium can be present on the surface of the solidsubstance in the fermentation broth, fermentation broth product, orcomposition at a density of at least about 1 Methylobacterium/20 squaremicrometers to about 1 Methylobacterium/2 square micrometers, of atleast about 1 Methylobacterium/10 square micrometers to about 1Methylobacterium/2 square micrometers, of at least about 1Methylobacterium/10 square micrometers to about 1 Methylobacterium/2square micrometers, or of at least about 1 Methylobacterium/5 squaremicrometers to about 1 Methylobacterium/2 square micrometers. Biphasicfermentation broths provided herein can comprise a liquid phase thatcontains non-adherent Methylobacterium. In certain embodiments, titersof non-adherent Methylobacterium in the liquid phase can be less thanabout 100,000, 10,000, or 1,000 CFU/ml.

Biphasic culture methods provided can yield fermentation broths withMethylobacterium at a titer of greater than about 5×10⁸ colony-formingunits per milliliter, at a titer of greater than about 1×10⁹colony-forming units per milliliter, at a titer of greater than about1×10¹⁰ colony-forming units per milliliter, at a titer of at least about3×10¹⁰ colony-forming units per milliliter. In certain embodiments,fermentation broths provided herein can comprise Methylobacterium at atiter of at least about 5×10⁸ colony-forming units per milliliter to atleast about 3×10¹⁰ colony-forming units per milliliter, at least about5×10⁸ colony-forming units per milliliter to at least about 4×10¹⁰colony-forming units per milliliter, or at least about 5×10⁸colony-forming units per milliliter to at least about 6×10¹⁰colony-forming units per milliliter. In certain embodiments,fermentation broths provided herein can comprise Methylobacterium at atiter of at least about 1×10⁹ colony-forming units per milliliter to atleast about 3×10¹⁰ colony-forming units per milliliter, at least about1×10⁹ colony-forming units per milliliter to at least about 4×10¹⁰colony-forming units per milliliter, or at least about 1×10⁹colony-forming units per milliliter to at least about 6×10¹⁰colony-forming units per milliliter. In certain embodiments,fermentation broths provided herein will comprise Methylobacterium at atiter of at least about 1×10¹⁰ colony-forming units per milliliter to atleast about 3×10¹⁰ colony-forming units per milliliter, at least about1×10¹⁰ colony-forming units per milliliter to at least about 4×10¹⁰colony-forming units per milliliter, or at least about 1×10¹⁰colony-forming units per milliliter to at least about 6×10¹⁰colony-forming units per milliliter. In certain embodiments,fermentation broths provided herein will comprise Methylobacterium at atiter of, at least about 3×10¹⁰ colony-forming units per milliliter toat least about 4×10¹⁰ colony-forming units per milliliter, or at leastabout 3×10¹⁰ colony-forming units per milliliter to at least about6×10¹⁰ colony-forming units per milliliter.

Solid substances with adherent Methylobacterium can be obtained asfermentation products can be used to make various compositions usefulfor treating plants or plant parts to improve plant yield, plant insectresistance, plant fungal disease resistance, and/or to improve lettuceproduction. In certain embodiments, the composition comprisesMethylobacterium and is depleted of substances that promote growth ofresident bacteria. Compositions provided herein comprisingMethylobacterium, solid substances with Methylobacterium grown thereon,or comprising emulsions with Methylobacterium grown therein can be usedto treat plants or plant parts. Plants, plant parts, and, in particular,plant seeds that have been at least partially coated or coated with thefermentation broth products or compositions comprising Methylobacteriumare thus provided. Also provided are processed plant products thatcontain the fermentation broth products or compositions withMethylobacterium or adherent Methylobacterium. Solid substances withadherent Methylobacterium can be used to make various compositions thatare particularly useful for treating plant seeds. Seeds that have beenat least partially coated with the fermentation broth products orcompositions are thus provided. Also provided are processed seedproducts, including, but not limited to, meal, flour, feed, and flakesthat contain the fermentation broth products or compositions providedherein. In certain embodiments, the processed plant product will benon-regenerable (i.e. will be incapable of developing into a plant). Incertain embodiments, the solid substance used in the fermentationproduct or composition that at least partially coats the plant, plantpart, or plant seed or that is contained in the processed plant, plantpart, or seed product comprises a solid substance and associated oradherent Methylobacterium that can be readily identified by comparing atreated and an untreated plant, plant part, plant seed, or processedproduct thereof. Partial coating of a plant, a plant part, or a seedincludes, but is not limited to coating at least about 5%, 10%, 20%,30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99%, or about 99.5% of thesurface area of the plant, plant part, or plant seed.

Methods of preparing a plant or plant seed treatment composition thatcomprises Methylobacterium and is depleted of substances that promotegrowth of resident bacteria on a plant or seed are also provided herein.Such methods can comprise (i) growing a mono-culture or co-culture ofMethylobacterium in media that comprises: (a) an aqueous phase; (b) aliquid phase and a solid phase; or (c) an emulsion, thereby obtaining aMethylobacterium-containing media; (ii) separating the Methylobacteriumfrom at least one other portion of the Methylobacterium-containingmedia; and (iii) reconstituting the Methylobacterium in a matrix lackingsubstances that promote growth of resident bacteria on a plant or seed.In certain embodiments, the separation step is effected bycentrifugation, filtration, or settling of theMethylobacterium-containing media and removal of excess liquid oremulsion therefrom. In certain embodiments where the Methylobacteriumare grown in the presence of a solid substance, the separation willprovide a fraction containing Methylobacterium with adherent growth tothe solid substance and some non-adherent Methylobacterium that can bereconstituted in the matrix. In certain embodiments, the substance thatpromotes growth of resident bacteria on a plant or seed is selected fromthe group consisting of a carbon source, a nitrogen source, aphosphorous source, a sulfur source, a magnesium source, andcombinations thereof. In certain embodiments, the matrix is a liquid, anemulsion, or one or more solids, and comprises an agriculturallyacceptable adjuvant and/or excipient. In certain embodiments; theMethylobacterium are grown in media comprising a liquid phase and asolid substance with adherent Methylobacterium grown thereon. The solidsubstance is separated from the liquid phase of theMethylobacterium-containing media, and the solid substance with adherentMethylobacterium grown thereon is reconstituted in the aforementionedmatrix. In certain embodiments, the matrix can be a liquid including,but not limited to, water, and aqueous buffer depleted of substancesthat promote growth of resident bacteria on a plant or seed, or anaqueous solution depleted of substances that promote growth of residentbacteria on a plant or seed.

In certain embodiments, the Methylobacterium sp. that improve lettuceproduction can be identified by testing newly isolated candidateMethylobacterium sp. for the presence of polymorphic nucleic acidsequences that are present in exemplary Methylobacterium sp. providedherein that improve lettuce production and that are absent fromMethylobacterium sp. provided herein that do not improve lettuceproduction. In certain embodiments, the polymorphic nucleic acidsequences that are present in the identified Methylobacterium sp. thatimprove lettuce production are also present in one or more of theexemplary Methylobacterium sp. isolates NLS0020, NLS0066, NLS0017,NLS0065, NLS0089, NLS0042, and NLS0068 provided herein that improvelettuce production but are absent from one or more of theMethylobacterium sp. isolates provided herein that do not improvelettuce production. In certain embodiments, the polymorphic nucleic acidsequences that are present in the identified Methylobacterium sp. thatimprove lettuce production are also present in one or more of theexemplary Methylobacterium sp. isolates NLS0020, NLS0066, NLS0017,NLS0065 and/or NLS0089 provided herein that improve lettuce productionwhen applied as seed treatments but are absent from one or more of theMethylobacterium sp. isolates provided herein that do not improvelettuce production when applied as seed treatments. In certainembodiments, the polymorphic nucleic acid sequences that are present inthe identified Methylobacterium sp. that improve lettuce production arealso present in one or more of the exemplary Methylobacterium sp.isolates NLS0020, NLS0017, NLS0042, and NLS0068 provided herein thatimprove lettuce production when applied as foliar treatments but areabsent from one or more of the Methylobacterium sp. isolates providedherein that do not improve lettuce production when applied as foliartreatments. In certain embodiments, the polymorphic nucleic acidsequences that are present in the identified Methylobacterium sp. thatimprove lettuce production are also present in two or more of theexemplary Methylobacterium sp. isolates NLS0020, NLS0066, NLS0017,NLS0065, NLS0089, NLS0042, and NLS0068 provided herein that improvelettuce production but are absent in two or more of the Methylobacteriumsp. isolates provided herein that do not improve lettuce production. Incertain embodiments, the polymorphic nucleic acid sequences that arepresent in the identified Methylobacterium sp. that improve lettuceproduction are also present in one or more of the exemplaryMethylobacterium sp. isolates NLS0020, NLS0066, NLS0017, NLS0065,NLS0089, NLS0042, and/or NLS0068 provided herein that improve lettuceproduction but are absent from all of the Methylobacterium sp. isolatesprovided herein that do not improve lettuce production. In certainembodiments, the polymorphic nucleic acid sequences present in theidentified Methylobacterium sp. that improve lettuce production arepresent in all of the exemplary Methylobacterium sp. isolates NLS0020,NLS0066, NLS0017, NLS0065, NLS0089, NLS0042, and NLS0068 provided hereinthat improve lettuce production but are absent in all of theMethylobacterium sp. isolates provided herein that do not improvelettuce production. Such nucleic acid polymorphisms that occur in theMethylobacterium sp. that improve lettuce production can include, butare not limited to, single nucleotide polymorphisms, RFLP, AFLP and/orother DNA variations such as repetitive sequences, insertion sequences,transposons, and genomic islands occurring as a result of insertions,deletions, and substitutions (Indels) in the bacterial genome whichincludes both the chromosomal DNA as well as any extrachromosomalnucleic acid elements that may be present in the Methylobacterium sp.that improve lettuce production. Such extrachromosomal nucleic acidelements include, but are not limited to, plasmids, bacteriophage DNA orRNA, and the like. Methods used to identify such nucleotidepolymorphisms include, but are not limited to, single base extension(SBE) techniques, allele specific hybridization (ASH), real-time PCRdetection (i.e. TaqMan™; U.S. Pat. Nos. 5,804,375; 5,538,848; 5,487,972;and 5,210,015, which are each incorporated herein by reference in theirentireties), combinations of ASH and RT-PCR (KASP™ detection systems,LGC Genomics, Middlesex, UK) and deep sequencing techniques (U.S. PatentAppl. No. 20120264632, incorporated herein by reference in itsentirety).

Also provided herein are compositions, methods of making thecompositions, and methods of using the compositions to improve lettuceproduction where the compositions or methods comprise or use any of thefollowing Methylobacterium sp. isolates provided in the following Table1 or derivatives of the isolates. In certain embodiments, suchderivatives can include variants but are not limited to, variants of theisolates obtained by selection, variants of the isolates selected bymutagenesis and selection, and genetically transformed isolates obtainedfrom the isolates.

TABLE 1 Methylobacterium sp. isolates USDA ARS NLS NRRL No.¹ NLS0017NRRL B-50931 NLS0020 NRRL B-50930 NLS0021 NRRL B-50939 NLS0037 NRRLB-50941 NLS0038 NRRL B-50942 NLS0042 NRRL B-50932 NLS0046 NRRL B-50929NLS0062 NRRL B-50937 NLS0064 NRRL B-50938 NLS0065 NRRL B-50935 NLS0066NRRL B-50940 NLS0068 NRRL B-50934 NLS0069 NRRL B-50936 NLS0089 NRRLB-50933 ¹Deposit number for strain to be deposited with the AGRICULTURALRESEARCH SERVICE CULTURE COLLECTION (NRRL) of the National Center forAgricultural Utilization Research, Agricultural Research Service, U.S.Department of Agriculture, 1815 North University Street, Peoria,Illinois 61604 U.S.A. under the terms of the Budapest Treaty on theInternational Recognition of the Deposit of Microorganisms for thePurposes of Patent Procedure. Subject to 37 CFR §1.808(b), allrestrictions imposed by the depositor on the availability to the publicof the deposited material will be irrevocably removed upon the grantingof any patent from this patent application.

Co-assigned patent applications that disclose additional specific usesof the Methylobacterium strains of Table 1 such as: (1) increasing cornyield (U.S. 61/911780, filed Dec. 4, 2013; and International Applicationclaiming benefit of the same filed on Dec. 4, 2014); (2) increasingsoybean yield (U.S. 61/911698, filed Dec. 4, 2013; and InternationalApplication claiming benefit of the same filed on Dec. 4, 2014); (3)improving tomato growth (U.S. 61/954,390, filed Mar. 17, 2014; andInternational Application claiming benefit of the same filed on Dec. 4,2014); (4) improving fruit maturation (U.S. 61/911577, filed Dec. 4,2013; and International Application claiming benefit of the same filedon Dec. 4, 2014); (5) providing fungal disease resistance (U.S.62/045,950, filed Sep. 4, 2014; U.S. 62/013,464, filed Jun. 17, 2014)and are each incorporated herein by reference in their entireties.Specifically incorporated herein by reference in their entireties arethe amino acid and genomic nucleic acid sequences of NLS017 and NLS066disclosed in the International Application for Compositions And MethodsFor Improved Tomato Growth, filed Dec. 4, 2014 and claiming benefit ofU.S. 61/954390, filed Mar. 17, 2014.

Also provided herein are Methylobacterium sp. that provide for improvedlettuce production where the Methylobacterium sp. have any of: (i) atleast one gene encoding at least one protein that is orthologous to aprotein having an amino acid sequence of SEQ ID NO: 1-5125; or (ii) atleast one gene encoding at least one protein that is orthologous to areference protein of Table 7. A Methylobacterium sp. has at least onegene that is orthologous to a protein having an amino acid sequence ofat least one of SEQ ID NO: 1-5125, or to the corresponding SEQ ID NO ofa reference protein of Table 7, when a chromosome and/or anyextrachromosomal DNA in that Methylobacterium sp. contains a geneencoding a protein that has at least 50%, at least 60%, at least 70%, atleast 80%, at least 90%, at least 95%, at least 97%, at least 98%, atleast 99%, or 100% sequence identity across the entire length of theamino acid sequence of at least one of SEQ ID NO: 1-5125. TheMethylobacterium sp. can also have at least two, three, four, six,eight, 10, 15, or 20 genes encoding proteins that are orthologous toproteins having an amino acid sequence of SEQ ID NO: 1-5125 or encodingproteins that are orthologous to the corresponding SEQ ID NO of areference protein of Table 7. In certain embodiments, theMethylobacterium sp. can contain at least one gene encoding a proteinthat is orthologous to a reference protein having the amino acidsequence of 13, 14, 23, 27, 28, 30, 40, 43, 44, 51, 52, 57, 76, 85, 127,197, 198, 199, 1094, 1100, 1106, 1114,1116, 1117, 1120, 1180, 2180,2190, 2463, 2467, 2468, 2471, 2510, 2515, 2676, 2971, 3357, 3370, 3372,3394, 3427, 3429, 3430, 3950, 3952, 3968, 3987, 3996, 4004, 4006, and/or4067 of Table 7. In certain embodiments, the Methylobacterium sp. cancontain at least one gene encoding a protein that is orthologous toreference protein having the amino acid sequence of SEQ ID NO: 13, 14,23, 1094, 1100, 1106, 2467, 2468, 3357, 3370, and/or 3968 of Table 7. Incertain embodiments, the Methylobacterium sp. can contain at least onegene encoding a protein that is orthologous to reference protein havingthe amino acid sequence of SEQ ID NO: 1100, 1116, 2471, 2971, and/or3950 of Table 7. Examples of proteins that are orthologous to SEQ ID NO:1094 include, but are not limited to, the orthologous proteinsidentified as transcriptional regulators that are provided in Table 7.Examples of proteins that are orthologous to SEQ ID NO: 23 include, butare not limited to, the orthologous proteins identified astranscriptional regulator XRE family proteins that are provided in Table7. Examples of proteins that are orthologous to SEQ ID NO: 1100 include,but are not limited to, proteins having the amino acid sequence of SEQID NO: 17, 1110, 2179, 2484, and 3367 that are similar to proteinsidentified as ABC transporter-like proteins. Examples of proteins thatare orthologous to SEQ ID NO: 1116 include, but are not limited to,proteins having the amino acid sequence of SEQ ID NO: 37, 1116, 2182,and 2521 that are similar to proteins identified as multidrugtransporter MatE. Examples of proteins that are orthologous to SEQ IDNO: 2471 include, but are not limited to, proteins having the amino acidsequence of SEQ ID NO: 10, 2471, 3356, and 3958 that are similar toproteins identified as arsenite efflux pump ACR proteins. Examples ofproteins that are orthologous to SEQ ID NO: 2971 include, but are notlimited to, proteins having the amino acid sequence of SEQ ID NO: 250,1309, 2263, and 2971 that are similar to proteins identified as membersof the LysR family transcriptional regulators. In certain embodiments,the Methylobacterium sp. has at least one gene that is orthologous to aprotein having an amino acid sequence of at least one of SEQ ID NO:1-5125, or to the corresponding SEQ ID NO of a reference protein ofTable 7, with the proviso that the gene is not found in M. extorquensAM1, M. extorquens PA1, or M. extorquens ME4. Compositions comprisingany of the aforementioned Methylobacterium sp. and an agriculturallyacceptable excipient, adjuvant, or combination thereof are also providedalong with lettuce seeds or leaves that are at least partially coatedwith such compositions and methods of using such compositions as seed orfoliar treatments to improve lettuce production.

A Methylobacterium sp. can be determined to contain a gene encoding aprotein that is orthologous to a protein having an amino acid sequenceof SEQ ID NO: 1-5125 by a variety of different techniques. In certainembodiments, a Methylobacterium sp. can be determined to contain a geneencoding a protein that is orthologous to a protein having an amino acidsequence of SEQ ID NO: 1-5125 by assembling a complete electronicgenomic sequence comprising chromosomal and extrachromosomal DNAsequences present in that Methylobacterium sp. with a computer andassociated software, and determining if any of the open reading frames(ORF) present in that DNA sequence encode a protein having theaforementioned percent sequence identity. In such embodiments, the ORFcan be identified by performing a six-way translation of theelectronically assembled sequence and querying the translated with anamino acid sequence of SEQ ID NO: 1-5125 or the corresponding SEQ ID NO:of a reference protein of Table 7. In other embodiments, the present orabsence of a given sequence within a Methylobacterium sp. an amino acidsequence of SEQ ID NO: 1-5125 or the corresponding SEQ ID NO: of areference protein of Table 7 can be determined by a nucleic acidanalysis or protein analysis technique. Examples of nucleic acidsequences that encode the proteins of SEQ ID NO:1-5125 include, but arenot limited to, SEQ ID NO: 5126-10250, respectively. Such nucleic acidanalyses include, but are not limited to, techniques based on nucleicacid hybridization, polymerase chain reactions, mass spectroscopy,nanopore based detection, combinations thereof, and the like. Proteinanalysis techniques include, but are not limited to, immuno-detection,mass spectroscopy, combinations thereof, and the like.

Compositions provided herein that are useful for treating lettuce plantsor plant parts that comprise Methylobacterium, and/or are depleted ofsubstances that promote growth of resident bacteria on a plant or seed,contain a solid substance with adherent Methylobacterium grown thereon,or that comprise emulsions with Methylobacterium grown therein can alsofurther comprise an agriculturally acceptable adjuvant or anagriculturally acceptable excipient. An agriculturally acceptableadjuvant or an agriculturally acceptable excipient is typically aningredient that does not cause undue phytotoxicity or other adverseeffects when exposed to a plant or plant part. In certain embodiments,the solid substance can itself be an agriculturally acceptable adjuvantor an agriculturally acceptable excipient so long as it is notbacteriocidal or bacteriostatic to the Methylobacterium. In otherembodiments, the composition further comprises at least one of anagriculturally acceptable adjuvant or an agriculturally acceptableexcipient. Any of the aforementioned compositions can also furthercomprise a pesticide. Pesticides used in the composition include, butare not limited to, an insecticide, a fungicide, a nematocide, and abacteriocide. In certain embodiments, the pesticide used in thecomposition is a pesticide that does not substantially inhibit growth ofthe Methylobacterium. As Methylobacterium are gram negative bacteria,suitable bacteriocides used in the compositions can include, but are notlimited to, bacteriocides that exhibit activity against gram positivebacteria but not gram negative bacteria. Compositions provided hereincan also comprise a bacteriostatic agent that does not substantiallyinhibit growth of the Methylobacterium. Bacteriostatic agents suitablefor use in compositions provided herein include, but are not limited to,those that exhibit activity against gram positive bacteria but not gramnegative bacteria. Any of the aforementioned compositions can also be anessentially dry product (i.e. having about 5% or less water content), amixture of the composition with an emulsion, or a suspension. Any of thecompositions provided herein can be used to coat or partially coat aplant, plant, part, or plant seed. Partial coating of a plant, a plantpart, or a seed includes, but is not limited to coating at least about5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99%, or about99.5% of the surface area of the plant, plant part, or plant seed.

Agriculturally acceptable adjuvants used in the compositions thatcomprise Methylobacterium include, but are not limited to, componentsthat enhance product efficacy and/or products that enhance ease ofproduct application. Adjuvants that enhance product efficacy can includevarious wetters/spreaders that promote adhesion to and spreading of thecomposition on plant parts, stickers that promote adhesion to the plantpart, penetrants that can promote contact of the active agent withinterior tissues, extenders that increase the half-life of the activeagent by inhibiting environmental degradation, and humectants thatincrease the density or drying time of sprayed compositions.Wetters/spreaders used in the compositions can include, but are notlimited to, non-ionic surfactants, anionic surfactants, cationicsurfactants, amphoteric surfactants, organo-silicate surfactants, and/oracidified surfactants. Stickers used in the compositions can include,but are not limited to, latex-based substances, terpene/pinolene, andpyrrolidone-based substances. Penetrants can include mineral oil,vegetable oil, esterified vegetable oil, organo-silicate surfactants,and acidified surfactants. Extenders used in the compositions caninclude, but are not limited to, ammonium sulphate, or menthene-basedsubstances. Humectants used in the compositions can include, but are notlimited to, glycerol, propylene glycol, and diethyl glycol. Adjuvantsthat improve ease of product application include, but are not limitedto, acidifying/buffering agents, anti-foaming/de-foaming agents,compatibility agents, drift-reducing agents, dyes, and waterconditioners. Anti-foaming/de-foaming agents used in the compositionscan include, but are not limited to, dimethopolysiloxane. Compatibilityagents used in the compositions can include, but are not limited to,ammonium sulphate. Drift-reducing agents used in the compositions caninclude, but are not limited to, polyacrylamides, and polysaccharides.Water conditioners used in the compositions can include, but are notlimited to, ammonium sulphate.

Methods of treating plants and/or plant parts with the fermentationbroths, fermentation broth products, and compositions comprisingMethylobacterium are also provided herein. Treated plants, and treatedplant parts obtained therefrom, include, but are not limited to, apepper, tomato, berry, or banana plant. Plant parts that are treatedinclude, but are not limited to, leaves, stems, flowers, roots, seeds,fruit, tubers, coleoptiles, and the like. Seeds or other propagules ofany of the aforementioned plants can be treated with the fermentationbroths, fermentation broth products, fermentation products, and/orcompositions provided herein.

In certain embodiments, plants and/or plant parts are treated byapplying the fermentation broths, fermentation broth products,fermentation products, and compositions that comprise Methylobacteriumas a spray. Such spray applications include, but are not limited to,treatments of a single plant part or any combination of plant parts.Spraying can be achieved with any device that will distribute thefermentation broths, fermentation broth products, fermentation products,and compositions to the plant and/or plant part(s). Useful spray devicesinclude a boom sprayer, a hand or backpack sprayer, crop dusters (i.e.aerial spraying), and the like. Spraying devices and or methodsproviding for application of the fermentation broths, fermentation brothproducts, fermentation products, and compositions to either one or bothof the adaxial surface and/or abaxial surface can also be used. Plantsand/or plant parts that are at least partially coated with any of abiphasic fermentation broth, a fermentation broth product, fermentationproduct, or compositions that comprise a solid substance withMethylobacterium adhered thereto are also provided herein. Also providedherein are processed plant products that comprise a solid substance withMethylobacterium adhered thereto. Any of the compositions providedherein can be used to coat or partially coat a plant, plant, part, orplant seed. Partial coating of a plant, a plant part, or a seedincludes, but is not limited to coating at least about 5%, 10%, 20%,30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99%, or about 99.5% of thesurface area of the plant, plant part, or plant seed

In certain embodiments, lettuce seeds are treated by exposing the seedsto the fermentation broths, fermentation broth products, fermentationproducts, and compositions that comprise Methylobacterium. Seeds can betreated with the fermentation broths, fermentation broth products, andcompositions provided herein by methods including, but not limited to,imbibition, coating, spraying, and the like. In certain embodiments,surface sterilized seeds are treated with a composition comprisingMethylobacterium. In certain embodiments, non-sterilized seeds (i.e.seeds that have not been subjected to surface sterilization) are treatedwith a composition comprising Methylobacterium that has been depleted ofsubstances that promote growth of resident microorganisms on the seed.Seed treatments can be effected with both continuous and/or a batch seedtreaters. In certain embodiments, the coated seeds may be prepared byslurrying seeds with a coating composition containing a fermentationbroth, fermentation broth product, or compositions that comprise thesolid substance with Methylobacterium and air drying the resultingproduct. Air drying can be accomplished at any temperature that is notdeleterious to the seed or the Methylobacterium, but will typically notbe greater than 30 degrees Centigrade. The proportion of coating thatcomprises a solid substance and Methylobacterium includes, but is notlimited to, a range of 0.1 to 25% by weight of the seed, 0.5 to 5% byweight of the seed, and 0.5 to 2.5% by weight of seed. Partial coatingof a seed can includes, but is not limited to coating at least about 5%,10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99%, or about99.5% of the surface area of the seed. In certain embodiments, a solidsubstance used in the seed coating or treatment will haveMethylobacterium adhered thereon. In certain embodiments, a solidsubstance used in the seed coating or treatment will be associated withMethylobacterium and will be a fermentation broth, fermentation brothproduct, or composition obtained by the methods provided herein. Variousseed treatment compositions and methods for seed treatment disclosed inU.S. Pat. Nos. 5,106,648, 5,512,069, and 8,181,388 are incorporatedherein by reference in their entireties and can be adapted for use withan active agent comprising the fermentation broths, fermentation brothproducts, or compositions provided herein. In certain embodiments, thecomposition used to treat the seed can contain agriculturally acceptableexcipients that include, but are not limited to, woodflours, clays,activated carbon, diatomaceous earth, fine-grain inorganic solids,calcium carbonate and the like. Clays and inorganic solids that can beused with the fermentation broths, fermentation broth products, orcompositions provided herein include, but are not limited to, calciumbentonite, kaolin, china clay, talc, perlite, mica, vermiculite,silicas, quartz powder, montmorillonite and mixtures thereof.Agriculturally acceptable adjuvants that promote sticking to the seedthat can be used include, but are not limited to, polyvinyl acetates,polyvinyl acetate copolymers, hydrolyzed polyvinyl acetates,polyvinylpyrrolidone-vinyl acetate copolymer, polyvinyl alcohols,polyvinyl alcohol copolymers, polyvinyl methyl ether, polyvinyl methylether-maleic anhydride copolymer, waxes, latex polymers, cellulosesincluding ethylcelluloses and methylcelluloses, hydroxymethylcelluloses, hydroxypropylcellulose, hydroxymethylpropylcelluloses,polyvinyl pyrrolidones, alginates, dextrins, malto-dextrins,polysaccharides, fats, oils, proteins, karaya gum, jaguar gum,tragacanth gum, polysaccharide gums, mucilage, gum arabics, shellacs,vinylidene chloride polymers and copolymers, soybean-based proteinpolymers and copolymers, lignosulfonates, acrylic copolymers, starches,polyvinylacrylates, zeins, gelatin, carboxymethylcellulose, chitosan,polyethylene oxide, acrylamide polymers and copolymers, polyhydroxyethylacrylate, methylacrylamide monomers, alginate, ethylcellulose,polychloroprene and syrups or mixtures thereof. Other usefulagriculturally acceptable adjuvants that can promote coating include,but are not limited to, polymers and copolymers of vinyl acetate,polyvinylpyrrolidone-vinyl acetate copolymer and water-soluble waxes.Various surfactants, dispersants, anticaking-agents, foam-controlagents, and dyes disclosed herein and in U.S. Pat. No. 8,181,388 can beadapted for use with an active agent comprising the fermentation broths,fermentation broth products, or compositions provided herein.

Provided herein are compositions that comprise Methylobacterium thatprovide improved lettuce production relative to untreated plants thathave not been exposed to the compositions. In certain embodiments, plantparts, including, but not limited to, a seed, a leaf, a fruit, a stem, aroot, a tuber, or a coleoptile can be treated with the compositionsprovided herein to improve lettuce production. Treatments orapplications can include, but are not limited to, spraying, coating,partially coating, immersing, and/or imbibing the plant or plant partswith the compositions provided herein. In certain embodiments, a seed, aleaf, a fruit, a stem, a root, a tuber, or a coleoptile can be immersedand/or imbibed with a liquid, semi-liquid, emulsion, or slurry of acomposition provided herein. Such seed immersion or imbibition can besufficient to provide for improved lettuce production in a treated plantor plant part in comparison to an untreated plant or plant part.Improved lettuce production includes, but is not limited, to increasedroot growth, increased leaf growth, increased seed production, and/orincreased total biomass relative to untreated plants. In certainembodiments, plant seeds can be immersed and/or imbibed for at least 1,2, 3, 4, 5, or 6 hours. Such immersion and/or imbibition can, in certainembodiments, be conducted at temperatures that are not deleterious tothe plant seed or the Methylobacterium. In certain embodiments, theseeds can be treated at about 15 to about 30 degrees Centigrade or atabout 20 to about 25 degrees Centigrade. In certain embodiments, seedimbibition and/or immersion can be performed with gentle agitation.

Compositions provided herein comprising Methylobacterium are thereforeexpected to be useful in improving lettuce production.

In certain embodiments, an amount of a composition provided herein thatis sufficient to provide for improved lettuce production can be acomposition with Methylobacterium at a titer of at least about 1×10⁶colony-forming units per milliliter, at least about 5×10⁶ colony-formingunits per milliliter, at least about 1×10⁷ colony-forming units permilliliter, at least about 5×10⁸ colony-forming units per milliliter, atleast about 1×10⁹ colony-forming units per milliliter, at least about1×10¹⁰ colony-forming units per milliliter, or at least about 3×10¹⁰colony-forming units per milliliter. In certain embodiments, an amountof a composition provided herein that is sufficient to provide forimproving lettuce production can be a composition with Methylobacteriumat a titer of about least about 1×10⁶ colony-forming units permilliliter, at least about 5×10⁶ colony-forming units per milliliter, atleast about 1×10⁷ colony-forming units per milliliter, or at least about5×10⁸ colony-forming units per milliliter to at least about 6×10¹⁰colony-forming units per milliliter of a liquid or an emulsion. Incertain embodiments, an amount of a composition provided herein that issufficient to provide for improving lettuce production can be afermentation broth product with a Methylobacterium titer of a solidphase of that product is at least about 5×10⁸ colony-forming units permilliliter to at least about 5×10¹³ colony-forming units ofMethylobacterium per gram of the solid phase. In certain embodiments, anamount of a composition provided herein that is sufficient to providefor improving lettuce production can be a composition withaMethylobacterium titer of at least about 1×10⁶ colony-forming units pergram, at least about 5×10⁶ colony-forming units per gram, at least about1×10⁷ colony-forming units per gram, or at least about 5×10⁸colony-forming units per gram to at least about 6×10¹⁰ colony-formingunits of Methylobacterium per gram of particles in the compositioncontaining the particles that comprise a solid substance wherein amono-culture or co-culture of Methylobacterium is adhered thereto. Incertain embodiments, an amount of a composition provided herein that issufficient to provide for improving lettuce production can be acomposition with aMethylobacterium titer of at least about 1×10⁶colony-forming units per mL, at least about 5×10⁶ colony-forming unitsper mL, at least about 1×10⁷ colony-forming units per mL, or at leastabout 5×10⁸ colony-forming units per mL to at least about 6×10¹⁰colony-forming units of Methylobacterium per mL in a compositioncomprising an emulsion wherein a mono-culture or co-culture of aMethylobacterium adhered to a solid substance is provided therein orgrown therein. In certain embodiments, an amount of a compositionprovided herein that is sufficient to provide for improving lettuceproduction can be a composition with aMethylobacterium titer of at leastabout 1×10⁶ colony-forming units per mL, at least about 5×10⁶colony-forming units per mL, at least about 1×10⁷ colony-forming unitsper mL, or at least about 5×10⁸ colony-forming units per mL to at leastabout 6×10¹⁰ colony-forming units of Methylobacterium per mL of in acomposition comprising an emulsion wherein a mono-culture or co-cultureof a Methylobacterium is provided therein or grown therein.

In certain embodiments, an amount of a composition provided herein thatis sufficient to provide for improved lettuce production can be acomposition with aMethylobacterium sp. at a titer of at least about1×10⁴ colony-forming units per milliliter, at least about 1×10⁵colony-forming units per milliliter, at least about 1×10⁶ colony-formingunits per milliliter, at least about 5×10⁶ colony-forming units permilliliter, at least about 1×10⁷ colony-forming units per milliliter, atleast about 5×10⁸ colony-forming units per milliliter, at least about1×10⁹ colony-forming units per milliliter, at least about 1×10¹⁰colony-forming units per milliliter, or at least about 3×10¹⁰colony-forming units per milliliter. In certain embodiments, an amountof a composition provided herein that is sufficient to provide forimproved lettuce production can be a composition with Methylobacteriumsp. at a titer of at least about 1×10⁴ colony-forming units permilliliter, at least about 1×10⁵ colony-forming units per milliliter,about least about 1×10⁶ colony-forming units per milliliter, at leastabout 5×10⁶ colony-forming units per milliliter, at least about 1×10⁷colony-forming units per milliliter, or at least about 5×10⁸colony-forming units per milliliter to at least about 6×10¹⁰colony-forming units per milliliter of a liquid or an emulsion. Incertain embodiments, an amount of a composition provided herein that issufficient to provide for improved lettuce production can be afermentation broth product with aMethylobacterium sp. titer of a solidphase of that product is at least about 1×10⁴ colony-forming units pergram, at least about 1×10⁵ colony-forming units per gram, at least about1×10⁶ colony-forming units per gram, at least about 5×10⁶ colony-formingunits per gram, at least about 1×10⁷ colony-forming units per gram, atleast about 5×10⁸ colony-forming units per gram, at least about 1×10⁹colony-forming units per gram, or at least about 5×10⁹ colony-formingunits per gram to at least about 6×10¹⁰ colony-forming units ofMethylobacterium per gram, at least about 1×10¹¹ colony-forming units ofMethylobacterium per gram, at least about 1×10¹² colony-forming units ofMethylobacterium per gram, at least about 1×10¹³ colony-forming units ofMethylobacterium per gram, or at least about 5×10¹³ colony-forming unitsof Methylobacterium per gram of the solid phase. In certain embodiments,an amount of a composition provided herein that is sufficient to providefor improved lettuce production can be a composition withaMethylobacterium titer of at least about 1×10⁶ colony-forming units pergram, at least about 5×10⁶ colony-forming units per gram, at least about1×10⁷ colony-forming units per gram, at least about 5×10⁸ colony-formingunits per gram, at least about 1×10⁹ colony-forming units per gram, orat least about 5×10⁹ colony-forming units per gram to at least about6×10¹⁰ colony-forming units of Methylobacterium per gram, at least about1×10¹¹ colony-forming units of Methylobacterium per gram, at least about1×10¹² colony-forming units of Methylobacterium per gram, at least about1×10¹³ colony-forming units of Methylobacterium per gram, or at leastabout 5×10¹³ colony-forming units of Methylobacterium per gram ofparticles in the composition containing the particles that comprise asolid substance wherein a mono-culture or co-culture of Methylobacteriumsp. is adhered thereto. In certain embodiments, an amount of acomposition provided herein that is sufficient to provide for improvedlettuce production can be a composition with a Methylobacterium titer ofat least about 1×10⁶ colony-forming units per mL, at least about 5×10⁶colony-forming units per mL, at least about 1×10⁷ colony-forming unitsper mL, or at least about 5×10⁸ colony-forming units per mL to at leastabout 6×10¹⁰ colony-forming units of Methylobacterium per mL in acomposition comprising an emulsion wherein a mono-culture or co-cultureof a Methylobacterium sp. adhered to a solid substance is providedtherein or grown therein. In certain embodiments, an amount of acomposition provided herein that is sufficient to provide for improvedlettuce production can be a composition with aMethylobacterium titer ofat least about 1×10⁶ colony-forming units per mL, at least about 5×10⁶colony-forming units per mL, at least about 1×10⁷ colony-forming unitsper mL, or at least about 5×10⁸ colony-forming units per mL to at leastabout 6×10¹⁰ colony-forming units of Methylobacterium per mL of in acomposition comprising an emulsion wherein a mono-culture or co-cultureof aMethylobacterium sp. is provided therein or grown therein.

In certain embodiments, compositions with a Methylobacterium sp. at atiter of at least about 1×10⁴ colony-forming units per milliliter, atleast about 1×10⁵ colony-forming units per milliliter, at least about1×10⁶ colony-forming units per milliliter, at least about 5×10⁶colony-forming units per milliliter, at least about 1×10⁷ colony-formingunits per milliliter, at least about 5×10⁸ colony-forming units permilliliter, at least about 1×10⁹ colony-forming units per milliliter, atleast about 1×10¹⁰ colony-forming units per milliliter, or at leastabout 3×10¹⁰ colony-forming units per milliliter are provided or used.In certain embodiments, compositions with Methylobacterium sp. at atiter of at least about 1×10⁴ colony-forming units per milliliter, atleast about 1×10⁵ colony-forming units per milliliter, about least about1×10⁶ colony-forming units per milliliter, at least about 5×10⁶colony-forming units per milliliter, at least about 1×10⁷ colony-formingunits per milliliter, or at least about 5×10⁸ colony-forming units permilliliter to at least about 6×10¹⁰ colony-forming units per milliliterof a liquid or an emulsion are provided. In certain embodiments,fermentation broth products with aMethylobacterium sp. titer of a solidphase of that product is at least about 1×10⁴ colony-forming units pergram, at least about 1×10⁵ colony-forming units per gram, at least about1×10⁶ colony-forming units per gram, at least about 5×10⁶ colony-formingunits per gram, at least about 1×10⁷ colony-forming units per gram, atleast about 5×10⁸ colony-forming units per gram, at least about 1×10⁹colony-forming units per gram, or at least about 5×10⁹ colony-formingunits per gram to at least about 6×10¹⁰ colony-forming units ofMethylobacterium per gram, at least about 1×10¹¹ colony-forming units ofMethylobacterium per gram, at least about 1×10¹² colony-forming units ofMethylobacterium per gram, at least about 1×10¹³ colony-forming units ofMethylobacterium per gram, or at least about 5×10¹³ colony-forming unitsof Methylobacterium per gram of the solid phase are provided. In certainembodiments, compositions with aMethylobacterium titer of at least about1×10⁶ colony-forming units per gram, at least about 5×10⁶ colony-formingunits per gram, at least about 1×10⁷ colony-forming units per gram, atleast about 5×10⁸ colony-forming units per gram, at least about 1×10⁹colony-forming units per gram, or at least about 5×10⁹ colony-formingunits per gram to at least about 6×10¹⁰ colony-forming units ofMethylobacterium per gram, at least about 1×10¹¹ colony-forming units ofMethylobacterium per gram, at least about 1×10¹² colony-forming units ofMethylobacterium per gram, at least about 1×10¹³ colony-forming units ofMethylobacterium per gram, or at least about 5×10¹³ colony-forming unitsof Methylobacterium per gram of particles in the composition containingthe particles that comprise a solid substance wherein a mono-culture orco-culture of Methylobacterium sp. is adhered thereto are provided. Incertain embodiments, compositions with a Methylobacterium titer of atleast about 1×10⁶ colony-forming units per mL, at least about 5×10⁶colony-forming units per mL, at least about 1×10⁷ colony-forming unitsper mL, or at least about 5×10⁸ colony-forming units per mL to at leastabout 6×10¹⁰ colony-forming units of Methylobacterium per mL in acomposition comprising an emulsion wherein a mono-culture or co-cultureof a Methylobacterium sp. adhered to a solid substance is providedtherein or grown therein are provided. In certain embodiments,compositions with a Methylobacterium titer of at least about 1×10⁶colony-forming units per mL, at least about 5×10⁶ colony-forming unitsper mL, at least about 1×10⁷ colony-forming units per mL, or at leastabout 5×10⁸ colony-forming units per mL to at least about 6×10¹⁰colony-forming units of Methylobacterium per mL of in a compositioncomprising an emulsion wherein a mono-culture or co-culture ofaMethylobacterium sp. is provided therein or grown therein is provided.In certain embodiments of any of the aforementioned compositions, theMethylobacterium sp. is selected from the group consisting of NLS0017(NRRL B-50931), NLS0020 (NRRL B-50930), NLS0021 (NRRL B-50939), NLS0037(NRRL B-50941), NLS0038 (NRRL B-50942), NLS0042 (NRRL B-50932), NLS0046(NRRL B-50929), NLS0062 (NRRL B-50937), NLS0064 (NRRL B-50938), NLS0065(NRRL B-50935), NLS0066 (NRRL B-50940), NLS0068 (NRRL B-50934), NLS0069(NRRL B-50936), NLS0089 (NRRL B-50933), and derivatives thereof. Incertain embodiments of any of the aforementioned compositions, thecomposition can further comprise an agriculturally acceptable adjuvant,an agriculturally acceptable excipient, or combination thereof. Incertain embodiments of any of the aforementioned compositions, theMethylobacterium sp. is selected from the group consisting of NLS0017(NRRL B-50931), NLS0020 (NRRL B-50930), NLS0021 (NRRL B-50939), NLS0037(NRRL B-50941), NLS0038 (NRRL B-50942), NLS0042 (NRRL B-50932), NLS0046(NRRL B-50929), NLS0062 (NRRL B-50937), NLS0064 (NRRL B-50938), NLS0065(NRRL B-50935), NLS0066 (NRRL B-50940), NLS0068 (NRRL B-50934), NLS0069(NRRL B-50936), NLS0089 (NRRL B-50933), derivatives thereof and alsocomprises an agriculturally acceptable adjuvant, excipient, orcombination thereof.

EXAMPLES

The following examples are included to demonstrate preferred embodimentsof the invention. It will be appreciated by those of skill in the artthat the techniques disclosed in the following examples representtechniques discovered by the Applicants to function well in the practiceof the invention, and thus can be considered to constitute preferredmodes for its practice. However, those of skill in the art should, inlight of the instant disclosure, appreciate that many changes can bemade in the specific embodiments that are disclosed, while stillobtaining like or similar results, without departing from the scope ofthe invention**.

Example 1 Culturing of PPFM Strains in a Liquid Growth MediaSupplemented with a Solid Substance

The liquid growth medium used to culture the PPFM cultures was a basesalts medium supplemented with glycerol, peptone, and diatomaceousearth. The base salts medium used was ammonium mineral salts (AMS)medium. AMS medium contains, per liter, 700 milligrams of dibasicpotassium phosphate anhydrous, 540 milligrams of monobasic potassiumphosphate anhydrous, one gram of magnesium sulfate heptahydrate, 500milligrams of ammonium chloride anhydrous, and 200 milligrams of calciumchloride dihydrate.

AMS base medium was prepared from three stock solutions, listed below:

Stock solution I: for one liter at SOX concentration

dibasic potassium phosphate, anhydrous 35 grams monobasic potassiumphosphate, anhydrous 27 grams

Stock solution II: for one liter at SOX concentration

magnesium sulfate heptahydrate 50 grams ammonium chloride, anhydrous 25grams

Stock solution III: for one liter at SOX concentration

calcium chloride dihydrate 10 grams

Stock solutions I, II, and III were autoclaved separately.

To prepare one liter of liquid AMS medium with glycerol, peptone, anddiatomaceous earth, the following were added to 920 ml of distilledwater:

20 ml of stock solution I

20 ml of stock solution II

20 ml of stock solution III

20 ml of a 50% glycerol stock solution

10 grams of peptone

2 grams of diatomaceous earth

The resulting solution with suspended diatomaceous earth was sterilizedby autoclaving.

Two liters of the above AMS medium were placed into a four-liter flask.Two milliliters of liquid culture PPFMs were added to the media toinoculate. The flask was then placed in an incubated shaker set to 240RPM and 30 degrees Celsius. The cultures were grown for six days andthen stored at 4 degrees Celsius for future use.

Example 2 Seed Inoculation of ‘Rex’ Lettuce to Identify PPFMs thatEnhance Root and Shoot Growth Seeding

A 104 cell Oasis HorticubeXL™ (bottom grooved, single dibble;Smithers-Oasis North America, Kent, Ohio, USA) was placed into a 1020flat without holes. Four cubes were removed in the center of grid toallow for bottom watering. The Oasis HorticubeXL™ was watered in so thatit was fully saturated, the shower setting with tempered water was used.One seed was placed in each cell for a total of 100 seeds per group.

Inoculation of Lettuce Seeds

The PPFM strains to be tested were grown as described in Example 1 in aliquid medium supplemented with a solid substance. In the biohood, thedesired amount of PPFM solution was pipetted into conical tubes (makesure to swirl/shake bottle vigorously before pipetting to suspendparticulates). A centrifuge was used to spin down at 3500 RPM for 15minutes at 23° C. While tubes were spun, a volume of tepid tap water wasmeasured out to bring the volume of each sample up to total volume.

Liquid was carefully poured off from each tube, careful to keep thepellet intact. The appropriate volume of tap water was added to eachtube to match its initial volume of PPFM solution. Water re-suspendedPPFMS were used as quickly as possible.

100 microliters of solution (PPFM solution for treated groups and tapwater for control groups) was pipetted onto the top of each seed. Afterevery 3 rows, the tube was capped and shaken to resuspend any PPFMs thatmay have settled to the bottom. Pipette tips were changed between eachgroup to avoid cross contamination. Tags were labeled and dated for eachflat and clear humidity domes place on top of flat. The flat were placedin a growth chamber with temperature settings at 20 C and 12 hour dayswith 200 micromole lighting.

Growth

After five to six days, domes were removed after seeds were germinated.Flats were bottom watered only and fertilized with Jack's™ 15-16-17 (JRPETERS, Inc. Allentown, Pa., USA) at every watering (approximately everyother day).

Daily repositioning of the flats was carried out to prevent potentialeffects on growth due to variations of light conditions in the growthchamber. Processing

Flats were harvested between two and three weeks. Clear humidity domeswere placed on each flat to prevent evapotranspiration during transport.Domes were left in place until flat was being processed. Each plant wascut directly below the cotyledons and immediately weighed on ananalytical balance. Observations

It was observed that some strains repeatedly showed an increase in shootbiomass of Lettuce seedlings when a seed was treated at the time ofplanting. Visual observations of root mass and development were alsomade, treated groups showed more growth at the time of harvest. Due tothe natural variance of biological systems all samples sizes were 98-100plants minimum and anything below 12% difference was not consideredsignificant.

Conclusion

It was apparent that strains NLS0017, NLS0020, NLS0066, NLS0065, andNLS0089 show an increase in wet weight of lettuce seedlings followingseed treatment. Strains NLS0069, NLS0037, NLS0038, and NLS0062 exhibitednegligible increases in wet weight in comparison to the controls. Alsonoted along with an increase in shoot biomass is a correspondingincrease in root development.

TABLE 2 Effects of seed treatments on lettuce growth seedling wet weight(mg) difference confidence strain titer control experimental (%)interval NLS0017 2.7E+08 226.18 306.36 35.45% 0.000 NLS0017 1.4E+08298.27 353.34 18.46% 0.012 NLS0017 2.7E+08 169.56 176.68 4.20% 0.567NLS0017 1.1E+09 98.92 167.51 69.34% 0.000 NLS0020 7.2E+08 226.18 274.4621.35% 0.027 NLS0020 1.2E+09 98.92 157.11 58.83% 0.000 NLS0020 1.2E+09462.20 614.72 33.00% 0.000 NLS0021 ND² 462.20 539.39 16.70% 0.008NLS0037 3.0E+08 226.18 258.68 14.37% 0.085 NLS0038 5.2E+07 462.20 514.9911.42% 0.070 NLS0042 2.1E+08 226.18 310.85 37.44% 0.000 NLS0042 1.1E+08169.56 189.46 11.73% 0.105 NLS0046 1.8E+09 462.20 511.78 10.73% 0.084NLS0062 1.8E+08 169.56 187.62 10.65% 0.121 NLS0064 ND² 169.56 157.67−7.01% 0.275 NLS0065 1.2E+08 169.56 211.92 24.98% 0.001 NLS0065 9.1E+0798.92 132.35 33.80% 0.000 NLS0066 5.9E+08 56.15 69.57 23.91% 0.000NLS0066 4.2E+08 546.61 665.46 21.74% 0.000 NLS0066 1.2E+08 98.92 129.8131.23% 0.000 NLS0068 3.1E+08 213.52 234.95 10.04% 0.029 NLS0069 5.6E+07226.18 244.25 7.99% 0.307 NLS0069 5.6E+07 298.27 332.53 11.49% 0.144NLS0089 1.5E+08 98.92 146.99 48.60% 0.000 NLS0089 ND² 462.20 600.8229.99% 0.000 ¹Each line represents data obtained from a separate flatsof plants obtained from treated seed versus control seed. ²ND: notdetermined.

Example 3 Foliar Application of ‘Rex’ Lettuce to Observe How PPFMsEffect Root and Shoot Growth Seeding

A 104 cell Oasis HorticubeXL (bottom grooved, single dibble) was placedinto a 1020 flat without holes. Four cubes were removed in the center ofgrid to allow for bottom watering. Oasis was watered in so that it wasfully saturated, the shower setting with tempered water was used. Oneseed was placed in each cell for a total of 100 seeds per group. Tagswere labeled and dated for each flat and clear humidity domes place ontop of flat. The flat were placed in a growth chamber with temperaturesettings at 20 C and 12-hour days with 200 micromole lighting.

Inoculation of Lettuce Seedlings

After five to six days, domes were removed after seeds had germinated.Plants were inoculated at this time, when only the cotyledons hademerged. The PPFM strains to be tested were grown as described inExample 1 in a liquid medium supplemented with a solid substance. ThePPFM strains to be tested were grown as described in Example 1 in aliquid medium supplemented with a solid substance. In the biohood, thedesired amount of PPFM solution was pipetted into conical tubes (makesure to swirl/shake bottle vigorously before pipetting to suspendparticulates). A centrifuge was used to spin down at 3500 RPM for 15minutes at 23° C. While tubes were spun, a volume of tepid tap water wasmeasured out to bring the volume of each sample up to total volume.

Liquid was carefully poured off from each tube, careful to keep thepellet intact. The appropriate volume of tap water was added to eachtube to match its initial volume of PPFM solution. Water re-suspendedPPFMS were used as quickly as possible.

100 mL of PPFM solution (tap water for control) was poured into a 1 LSolo™ Handheld Sprayer (Solo™, Newport News, Va., USA). The flat wasremoved from the group to avoid cross contamination. The finest mistsetting was used and an even coat of solution was sprayed over the topof the seedlings, ensuring even coverage across the entire flat. Foreach group this was repeated, using appropriate treatment. Growth

Flats were bottom watered only and fertilized with Jack's™ 15-16-17 (JRPETERS, Inc. Allentown, Pa., USA) at every watering (approximately everyother day). Daily repositioning of the flats was carried out to preventpotential effects on growth due to variations of light conditions in thegrowth chamber.

Processing

Flats were harvested between two and three weeks. Clear humidity domeswere placed on each flat to prevent evapotranspiration during transport.Domes were left in place until flat was being processed. Each plant wascut directly below the cotyledons and immediately weighed on ananalytical balance.

Observations

It was been observed that some strains repeatedly show an increase inshoot biomass of Lettuce seedlings when the seedling was treated at thecotyledon stage. Visual observations of root mass and development werealso made, that treated groups showed more growth at the time ofharvest. Due to the natural variance of biological systems all samplessizes were a 98-100 plants minimum and anything below 12% difference wasnot considered significant.

Conclusion

It is apparent that strains NLS0042, NLS0017, NLS0020, and NLS0068 showan increase in wet weight of lettuce seedlings following foliarapplication. Strains NLS0069, NLS0037, NLS0038, and NLS0062 exhibitednegligible increases in wet weight in comparison to the controls. Alsonoted along with an increase in shoot biomass is a correspondingincrease in root development.

TABLE 3 Effects of foliar treatments on lettuce growth seedling wetweight (mg) difference confidence strain titers control experimental (%)interval NLS0017 1.4E+08 197.04 213.76 8.49% 0.075 NLS0017 1.1E+09157.72 211.03 33.81% 0.000 NLS0020 2.2E+08 104.41 145.95 39.79% 0.000NLS0020 7.2E+08 205.34 247.12 20.34% 0.030 NLS0020 1.2E+09 280.84 260.95−7.08% 0.224 NLS0021 1.6E+07 157.72 178.46 13.15% 0.021 NLS0037 ND²197.04 198.93 0.96% 0.846 NLS0038 7.4E+07 197.04 186.04 −5.58% 0.250NLS0042 9.3E+07 103.36 127.05 22.92% 0.000 NLS0042 2.1E+08 205.34 235.9214.89% 0.095 NLS0042 6.4E+07 298.27 331.62 11.18% 0.138 NLS0042 1.1E+08157.72 196.12 24.35% 0.000 NLS0046 1.8E+09 157.72 195.03 23.66% 0.000NLS0062 ND² 280.84 243.09 −13.44% 0.018 NLS0064 ND² 205.34 240.47 17.10%0.042 NLS0064 ND² 298.27 306.88 2.89% 0.691 NLS0065 4.2E+08 197.04214.59 8.91% 0.077 NLS0066 5.9E+08 205.34 241.92 17.81% 0.035 NLS00661.2E+08 280.84 166.98 −40.54% 0.000 NLS0068 1.7E+08 104.41 204.26 95.65%0.000 NLS0068 1.6E+08 205.34 288.46 40.47% 0.000 NLS0068 3.1E+08 298.27296.68 −0.53% 0.944 NLS0068 3.1E+08 280.84 264.65 −5.76% 0.337 NLS00683.1E+08 157.72 183.84 16.56% 0.010 NLS0069 4.5E+07 99.85 103.54 3.70%0.711 NLS0089 1.3E+09 280.84 282.94 0.75% 0.896 ¹Each line representsdata obtained from a separate flat of treated versus control plants.²ND: not determined.

Example 4 Identification of Nucleic Acid Polymorphisms Present inMethylobacterium that Improve Lettuce Production

Whole genome sequencing libraries for the Illumina™ high-throughputsequencing platform are generated for Methylobacterium sp. isolatesprovided in Table 1 using Illumina TRUSEQ™ or NEXTERA™ DNA samplepreparation kits (described on the internet sitesres.illumina.com/documents/products/datasheets/datasheet_truseq_dna_sample_prep_kits.pdfandres.illumina.com/documents/products/datasheets/datasheet_nextera_dna_sample_prep.pdf)using the methods described by the manufacturer. The resultant librariesare then subjected to pyrosequencing (Siqueira J F et al. J OralMicrobiol. 2012; 4: 10.3402/jom.v4i0.10743). Rawpyrosequencing-generated genomic sequence data are subjected to adaptor-and quality-based trimming for quality control. Whole-genome ShotgunSequence Assembly (1) is achieved by assembling quality-passed datausing the de novo assembler Velvet (2). For gene finding and annotation,reference training data is leveraged from TIGRFAM (9), Pfam, COG (10),and UniRef100 (11). The rRNAs are identified with RNAmmer (5),protein-coding genes are identified with Glimmer (3) or Maker (6), andtRNAs are identified with tRNAscan-SE (4). Gene functions are assignedwith blastx (7), blastp (7), HMMER (8), and InterProScan againstcomprehensive protein databases described above (Reference Data).

Detection of polymorphisms (SNP or other DNA variations occurring as aresult of insertions, deletions, and substitutions (Indels)) in theMethylobacterium sp. isolates of Table 1 is performed with BWA (12) andthe Samtools suite (on the internet at samtools.sourceforge.net/),structural variation is identified with BreakDancer (on the internet atbreakdancer.sourceforge.net/) and CoGE (on the internet atgenomevolution.org/CoGe/). Polymorphisms diagnostic for Methylobacteriumthat provide for improved lettuce production are identified bycomparisons of the sequences of exemplary Methylobacterium isolatesNLS0020, NLS0066, NLS0017, NLS0065, NLS0089, NLS0042, and/or NLS0068that improve lettuce production but that are absent from one or moreMethylobacterium isolates that do not improve lettuce production.Polymorphisms present in exemplary Methylobacterium isolates NLS0020,NLS0066, NLS0017, NLS0065, NLS0089, NLS0042, and/or NLS0068 that improvelettuce production but that are absent in exemplary Methylobacteriumisolates that do not improve lettuce production are then used toidentify other Methylobacterium isolates that improve lettuceproduction.

REFERENCES FOR EXAMPLE 4

-   1. Miller J R, Koren S, Sutton G (2010) Assembly algorithms for    next-generation sequencing data. Genomics 95: 315-327.-   2. Zerbino D R, Birney E (2008) Velvet: algorithms for de novo short    read assembly using de Bruijn graphs. Genome Res 18: 821-829.-   3. Delcher A L, Bratke K A, Powers E C, Salzberg S L (2007)    Identifying bacterial genes and endosymbiont DNA with Glimmer.    Bioinformatics 23: 673-679.-   4. Lowe T M, Eddy S R (1997) tRNAscan-SE: a program for improved    detection of transfer RNA genes in genomic sequence. Nucleic Acids    Res 25: 955-964.-   5. Lagesen K, Hallin P, Rodland E A, Staerfeldt H H, Rognes T, et    al. (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA    genes. Nucleic Acids Res 35: 3100-3108.-   6. Cantarel B, Korf I, Robb S, et al. (2008) MAKER: An easy-to-use    annotation pipeline designed for emerging model organism genomes.    Genome Research 18: 188-196.-   7. Altschul S F, Madden T L, Schaffer A A, Zhang J, Zhang Z, et    al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein    database search programs. Nucleic Acids Res 25: 3389-3402.-   8. Eddy S R (2009) A new generation of homology search tools based    on probabilistic inference. Genome Inform 23: 205-211.-   9. Haft D H, Selengut J D, White O (2003) The TIGRFAMs database of    protein families. Nucleic Acids Res 31: 371-373.-   10. Tatusov R L, Fedorova N D, Jackson J D, Jacobs A R, Kiryutin B,    et al. (2003) The COG database: an updated version includes    eukaryotes. BMC Bioinformatics 4: 41.-   11. Suzek B E, Huang H, McGarvey P, Mazumder R, Wu C H (2007)    UniRef: comprehensive and non-redundant UniProt reference clusters.    Bioinformatics 23: 1282-1288.-   12. Li H. and Durbin R. (2009) Fast and accurate short read    alignment with Burrows-Wheeler Transform. Bioinformatics,    25:1754-60.

Example 5 Seed Inoculation of ‘Flandria’ Lettuce with PPFMs IncreasesShoot and Root Biomass Seeding

A 276 cell sheet of Oasis HORTICUBES® (1-inch Thin-Cut; Smithers-OasisNorth America, Kent, Ohio, USA) was placed into a 1020 mesh flat. Theflat was divided in half with a piece of plastic to allow for two groupsper flat. The Oasis HORTICUBES® were watered to full saturation.Flandria lettuce seed from Rijk Zwaan USA (Salinas, Calif., USA) wasused. One seed was placed in each cell for a total of 132 or 144 seedsper group.

Inoculation of Lettuce Seeds

The PPFM strains to be tested were grown as described in Example 1 in aliquid medium supplemented with diatomaceous earth at 2 grams/liter. Atthe bench, the desired amount of PPFM solution was pipetted into conicaltubes (making sure to swirl/shake bottle vigorously before pipetting tosuspend particulates). A centrifuge was used to pellet the cells at 7500RPM for 5 minutes at 23° C. The supernatant was discarded, and the PPFMpellets were resuspended in an equal volume of water.

100 microliters of solution (PPFM solution for treated groups and tapwater for control groups) were pipetted onto the top of each seed. Thetube was shaken periodically to keep the PPFM cells in suspension. Clearhumidity domes were placed over each flat. The flats were placed in agreenhouse with temperature settings of 30° C. during the day, 28° C. atnight and with a 16-hour day length attained with using supplementallight as necessary.

Growth

After two to three days after planting, the seeds had germinated, andthe humidity domes were removed. The flats were top watered andfertilized with Jack's™ 15-16-17 (JR PETERS, Inc. Allentown, Pa., USA)at every watering. Daily repositioning of the flats was carried out toprevent potential effects on growth due to variations of lightconditions in the growth chamber.

Processing

The lettuce seedlings were harvested at 10 days after planting. Eachplant was cut directly below the cotyledons and immediately weighed onan analytical balance.

Observations

It was observed that some strains repeatedly showed an increase in shootbiomass of the lettuce seedlings following seed treatment. Visualobservations of root mass and development were also made, and it wasnoted that treated groups showed more growth at the time of harvest. Theoutside row of each group was not harvested in order to eliminate anyedge effects in the flats.

Conclusion

It was apparent that PPFM strains NLS0017, NLS0020, NLS0066 and NLS0068showed a reproducible and statistically significant increase in the wetweight of lettuce seedlings following seed treatment. Also noted alongwith an increase in shoot biomass was a corresponding increase in rootdevelopment.

TABLE 4 Results for Seed inoculation of ‘Flandria’ Lettuce seedling wetweight Titer Control Experimental Difference confidence Strain (CFU/mL)(Water) (PPFM) (%) interval NLS0017 1.1E+09 103.38 152.14 47.16% 0.000NLS0017 1.1E+09 90.98 174.23 91.51% 0.000 NLS0017 1.1E+09 45.47 80.7477.57% 0.000 NLS0017 1.1E+09 101.46 174.29 71.78% 0.000 NLS0017 1.1E+09265.34 296.75 11.84% 0.000 NLS0020 1.2E+09 103.38 123.00 18.98% 0.000NLS0020 1.2E+09 90.98 174.92 92.27% 0.000 NLS0020 1.2E+09 45.47 72.2158.80% 0.000 NLS0020 1.2E+09 41.85 62.27 48.79% 0.000 NLS0020 1.2E+09195.98 232.44 18.60% 0.000 NLS0020 1.2E+09 89.68 121.69 35.68% 0.000NLS0020 1.2E+09 136.75 171.62 25.50% 0.000 NLS0020 1.2E+09 69.18 141.55104.59% 0.000 NLS0020 1.2E+09 38.38 63.65 65.84% 0.000 NLS0020 1.2E+0949.53 85.78 73.18% 0.000 NLS0037 not 183.18 199.05 8.67% 0.008determined NLS0037 1.8E+08 68.26 136.58 100.08% 0.000 NLS0038 5.2E+07183.18 201.56 10.03% 0.007 NLS0038 5.2E+07 68.26 108.01 58.23% 0.000NLS0038 5.2E+07 129.32 154.95 19.82% 0.000 NLS0042 1.1E+08 59.84 110.0483.90% 0.000 NLS0042 1.1E+08 183.18 186.49 1.81% 0.650 NLS0042 1.1E+0868.26 99.76 46.15% 0.000 NLS0062 3.6E+07 129.32 156.18 20.77% 0.000NLS0062 3.6E+07 140.95 190.36 35.06% 0.000 NLS0064 4.5E+08 129.32 158.5822.63% 0.000 NLS0064 4.5E+08 140.95 231.99 64.60% 0.000 NLS0065 3.7E+07140.95 211.13 49.80% 0.000 NLS0066 1.2E+08 103.38 180.71 74.80% 0.000NLS0066 1.2E+08 90.98 163.37 79.57% 0.000 NLS0066 1.2E+08 45.47 96.07111.28% 0.000 NLS0066 1.2E+08 91.32 114.02 24.86% 0.000 NLS0066 1.2E+08209.04 279.74 33.83% 0.000 NLS0068 2.1E+08 68.26 98.67 44.55% 0.000NLS0068 1.7E+08 129.32 181.12 40.06% 0.000 NLS0068 1.7E+08 140.95 217.8954.59% 0.000 NLS0069 1.6E+08 59.84 113.78 90.15% 0.000 NLS0069 5.6E+0768.26 75.17 10.12% 0.095 NLS0069 1.5E+08 129.32 164.10 26.89% 0.000NLS0089 3.0E+07 140.95 225.72 60.14% 0.000

REFERENCES

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Green, P. N. 2005. Methylobacterium. In Brenner, D. J., N. R.    Krieg, and J. T. Staley (eds.). “Bergey's Manual of Systematic    Bacteriology. Volume two, The Proteobacteria. Part C, The alpha-,    beta-, delta-, and epsilonproteobacteria.” Second edition. Springer,    New York. Pages 567-571.-   7. Green, P. N. 2006. Methylobacterium. In Dworkin, M., S.    Falkow, E. Rosenberg, K.-H. Schleifer, and E. Stackebrandt (eds.).    “The Prokaryotes. A Handbook on the Biology of Bacteria. Volume 5.    Proteobacteria: Alpha and Beta Subclasses.” Third edition. Springer,    New York. Pages 257-265.-   8. Holland, M. A. 1997. Methylobacterium and plants. Recent. Res.    Devel. in Plant Physiol. 1: 207-213.-   9. Holland, M. A., and J. C. Polacco. 1994. PPFMs and other covert    contaminants: Is there more to plant physiology than just plant?    Annu. Rev. Plant Physiol. Plant Mol. Biol. 45: 197-209.-   10. Kutschera, U. 2007. Plant-associated methylobacteria as    co-evolved phytosymbionts. A hypothesis. Plant Signal Behay. 2:    74-78.-   11. Lidstrom, M. E. 2006. Aerobic methylotrophic prokaryotes. In    Dworkin, M., S. Falkow, E. Rosenberg, K.-H. Schleifer, and E.    Stackebrandt (eds.). “The Prokaryotes. A Handbook on the Biology of    Bacteria. Volume 2. Ecophysiology and biochemistry.” Third edition.    Springer, New York. Pages 618-634.-   12. Madhaiyan, M., S. Poonguzhali, H. S. Lee, K. Hari, S. P.    Sundaram, and T. M. Sa. 2005. Pink-pigmented facultative    methylotrophic bacteria accelerate germination, growth and yield of    sugarcane clone Co86032 (Saccharum officinarum L.) Biol. Fertil.    Soils 41: 350-358.-   13. Madhaiyan, M., S. Poonguzhali, M. Senthilkumar, S. Seshadri, H.    Chung, J. Yang, S. Sundaram, and T. Sa. 2004. Growth promotion and    induction of systemic resistance in rice cultivar CO-47 (Oryza    sativa L.) by Methylobacterium spp. Bot. Bull. Acad. Sin. 45:    315-324.-   14. Madhaiyan, M., S. Poonguzhali, and T. Sa. 2007. Influence of    plant species and environmental conditions on epiphytic and    endophytic pink-pigmented facultative methylotrophic bacterial    populations associated with field-grown rice cultivars. J Microbiol    Biotechnol. 2007 October; 17(10):1645-54.-   15. Stanier, R. Y., N. J. Palleroni, and M. Doudoroff. 1966. The    aerobic pseudomonads: A taxonomic study. J. Gen. Microbiol. 43:    159-271.-   16. Sy, A., Giraud, E., Jourand, P., Garcia, N., Willems, A., De    Lajudie, P., Prin, Y., Neyra, M., Gillis, M., Boivin-Masson,C., and    Dreyfus, B. 2001. Methylotrophic Methylobacterium Bacteria Nodulate    and Fix Nitrogen in Symbiosis with Legumes. Jour. Bacteriol.    183(1):214-220,-   17. Sy, A., A. C. J. Timmers, C. Knief, and J. A. Vorholt. 2005.    Methylotrophic metabolism is advantageous for Methylobacterium    extorquens during colonization of Medicago truncatula under    competitive conditions. Appl. Environ. Microbiol. 71: 7245-7252.-   18. Vogel, H. J., and D. M. Bonner. 1956. Acetylornithinase of    Escherichia coli: Partial purification and some properties. J. Biol.    Chem. 218: 97-106.-   19. Vogel, H. J. 1956. A convenient growth medium for Neurospora    (Medium N). Microbial Genet Bull 13: 42-43-   20. Whittenbury, R., S. L. Davies, and J. F. Wilkinson. 1970.    Enrichment, isolation and some properties of methane-utilizing    bacteria. J. Gen. Microbiol. 61: 205-218.-   21. Vuilleumier S, Chistoserdova L, Lee M C, Bringel F, Lajus A,    Zhou Y, Gourion B, Barbe V, Chang J, Cruveiller S, Dossat C, Gillett    W, Gruffaz C, Haugen E, Hourcade E, Levy R, Mangenot S, Muller E,    Nadalig T, Pagni M, Penny C, Peyraud R, Robinson D G, Roche D, Rouy    Z, Saenampechek C, Salvignol G, Vallenet D, Wu Z, Marx C J, Vorholt    J A, Olson M V, Kaul R, Weissenbach J, Medigue C, Lidstrom M E.    Methylobacterium genome sequences: a reference blueprint to    investigate microbial metabolism of Cl compounds from natural and    industrial sources. 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PubMed PMID: 20700590.

Example 6 Seed Inoculation of ‘Rex’ Lettuce with PPFMs Increases Shootand Root Biomass

Seeding

A 276 cell sheet of Oasis HORTICUBES® (1-inch Thin-Cut; Smithers-OasisNorth America, Kent, Ohio, USA) was placed into a 1020 mesh flat. Theflat was divided in half with a piece of plastic to allow for two groupsper flat. The Oasis HORTICUBES® were watered to full saturation. Rexlettuce seed was used. One seed was placed in each cell for a total of132 or 144 seeds per group.

Inoculation of Lettuce Seeds

The PPFM strains to be tested were grown as described in Example 1 in aliquid medium supplemented with diatomaceous earth at 2 grams/liter. Atthe bench, the desired amount of PPFM solution was pipetted into conicaltubes (making sure to swirl/shake bottle vigorously before pipetting tosuspend particulates). A centrifuge was used to pellet the cells at 7500RPM for 5 minutes at 23° C. The supernatant was discarded, and the PPFMpellets were resuspended in an equal volume of water.

100 microliters of solution (PPFM solution for treated groups and tapwater for control groups) were pipetted onto the top of each seed. Thetube was shaken periodically to keep the PPFM cells in suspension. Clearhumidity domes were placed over each flat. The flats were placed in agreenhouse with temperature settings of 30° C. during the day, 28° C. atnight and with a 16-hour day length attained with using supplementallight as necessary.

Growth

After two to three days after planting, the seeds had germinated, andthe humidity domes were removed. The flats were top watered andfertilized with Jack's™ 15-16-17 (JR PETERS, Inc. Allentown, Pa., USA)at every watering. Daily repositioning of the flats was carried out toprevent potential effects on growth due to variations of lightconditions in the growth chamber.

Processing

The lettuce seedlings were harvested at 10 days after planting. Eachplant was cut directly below the cotyledons and immediately weighed onan analytical balance.

Observations

It was observed that some strains repeatedly showed an increase in shootbiomass of the lettuce seedlings following seed treatment. Visualobservations of root mass and development were also made, and it wasnoted that treated groups showed more growth at the time of harvest. Theoutside row of each group was not harvested in order to eliminate anyedge effects in the flats. The results are as shown in the followingTable.

TABLE 5 avg % Increase in Shoot Biomass in comparison # of Strain tocontrol tests NLS0062 44.00% 3 NLS0020 37.73% 3 NLS0042 33.82% 4 NLS004630.86% 3 NLS0068 30.83% 3 NLS0038 29.43% 3 NLS0089 29.16% 3 NLS001728.53% 5 NLS0021 28.27% 3 NLS0037 26.02% 3 NLS0066 25.63% 3 NLS006523.35% 3 NLS0064 21.88% 3 NLS0069 4.87% 3

Conclusion

It was apparent that PPFM strains NLS0017, NLS0020, NLS21, NLS0037,NLS0038, NLS42, NLS46, NLS62, NLS64, NLS0065, NLS0066, NLS0068, andNLS0089 showed a reproducible and statistically significant increase inthe wet weight of lettuce seedlings following seed treatment. Also notedalong with an increase in shoot biomass was a corresponding increase inroot development.

Example 7 Flandria Seed Tests

Flandria lettuce seed were treated with the indicated PPFM isolatesessentially as described in Example 5 to yield the following results.

TABLE 6 wet weight (mg) strain control experimental difference CINLS0017 103.38 152.14 47.16% 0.000 NLS0017 90.98 174.23 91.51% 0.000NLS0017 45.47 80.74 77.57% 0.000 NLS0017 101.46 174.29 71.78% 0.000NLS0017 265.34 296.75 11.84% 0.000 NLS0017 99.82 163.01 63.30% 0.000NLS0020 103.38 123.00 18.98% 0.000 NLS0020 90.98 174.92 92.27% 0.000NLS0020 45.47 72.21 58.80% 0.000 NLS0020 41.85 62.27 48.79% 0.000NLS0020 195.98 232.44 18.60% 0.000 NLS0020 89.68 121.69 35.68% 0.000NLS0020 136.75 171.62 25.50% 0.000 NLS0020 69.18 141.55 104.59%  0.000NLS0020 38.38 63.65 65.84% 0.000 NLS0020 49.53 85.78 73.18% 0.000NLS0037 59.84 109.56 83.10% 0.000 NLS0037 183.18 199.05  8.67% 0.008NLS0037 68.26 136.58 100.08%  0.000 NLS0037 97.72 156.97 60.63% 0.000NLS0037 91.74 130.58 42.34% 0.000 NLS0037 99.08 108.96  9.97% 0.030NLS0037 61.72 120.61 95.41% 0.000 NLS0042 59.84 110.04 83.90% 0.000NLS0042 183.18 184.47  0.70% 0.650 NLS0042 68.26 99.76 46.15% 0.000NLS0042 61.72 109.42 77.28% 0.000 NLS0065 140.95 211.13 49.80% 0.000NLS0065 61.72 109.38 77.22% 0.000 NLS0065 86.75 154.51 78.11% 0.000NLS0065 97.67 99.42  1.79% 0.691 NLS0066 103.38 180.71 74.80% 0.000NLS0066 90.98 163.37 79.57% 0.000 NLS0066 45.47 96.07 111.28%  0.000NLS0066 91.32 114.02 24.86% 0.000 NLS0066 209.04 279.74 33.83% 0.000NLS0066 99.82 101.20  1.38% 0.920 NLS0135 223.15 227.21  1.82% 0.588NLS0135 90.94 111.89   23% 0.000 NLS0135 145.2 118.14  −19% 0.000NLS0071 223.15 220.13 −1.35% 0.716 NLS0071 90.94 107.2   18% 0.000NLS0071 145.2 129.62  −11% 0.002 NLS0109 223.15 215.45 −3.45% 0.316NLS0109 90.94 109.91   21% 0.000 NLS0109 145.2 126.9  −13% 0.001 NLS0142223.15 197.98 −11.28%  0.002 NLS0142 90.94 94.89    4% 0.324 NLS0142145.2 121.09  −17% 0.000

It was evident that the PPFM strains NLS0017, NLS0037, NLS0066, NLS0020,NLS0042, NLS0065, NLS0089, NLS0046, NLS0021. NLS0069, NLS0068, NLS0064,NLS0062, and NLS0038 could provide for increased lettuce biomassrelative to control treatments.

Example 8 Identification of Orthologous Genes present inMethylobacterium sp. that can Improve Lettuce Production

The PPFM strains listed in Table 1 were grown on solid agar mediacomprising Ammonium Mineral Salts (AMS) plus glycerol and peptone at 30°C. for 5 days, essentially as described in co-assigned U.S. PatentApplication Publication No. US20130324407 and incorporated herein byreference in its entirety. Genomic DNA was extracted using MO-BIO(Carlsbad, Calif.) Ultra Clean Microbial DNA Isolation kit, and 1 μg ofhigh quality DNA was used for Illumina Nextera XT library preparationfollowed by Illumina 2×100 paired-end sequencing on a HiSeq2000 system.Raw Illumina genomic sequence data were subjected to adaptor- andquality-based trimming for quality control. Whole-genome ShotgunSequence Assembly was achieved by assembling quality-passed data usingthe de novo assembler SPADES (33). For gene finding and annotation,reference training data was leveraged from TIGRFAM (9), Pfam, COG (10),and UniRef100 (11). The rRNAs were identified with RNAmmer (5),protein-coding genes were identified with Glimmer (3) and Maker (6), andtRNAs were identified with tRNAscan-SE (4). Gene functions were assignedwith blastx (7), blastp (7), HMMER (8), and InterProScan againstcomprehensive protein databases described above (Reference Data).Detection of polymorphisms (SNP or other DNA variations occurring as aresult of insertions, deletions, and substitutions (Indels)) in theMethylobacterium sp. isolates was performed with BWA (12) and theSamtools suite (on the internet at samtools.sourceforge.net/) and theGenome Analysis Toolkit (GATK, on the world wide web internet site“broadinstitute.org/gatk/”), structural variation was identified withBreakDancer (on the internet at breakdancer.sourceforge.net/) and CoGE(on the internet at genomevolution.org/CoGe/).

Genes that encoded open reading frames were predicted from the assembledwhole genomic sequences of NLS0017, NLS0020, NLS0037, NLS0042, NLS0065,NLS0066, NLS0135, NLS0071, NLS0109, and NLS0142 essentially as describedabove. Within and between genome orthologous genes were clustered usingOrthoMCL (available on the world wide web internet site“orthomcl.org/orthomc/”). Putative functional annotations were assignedto gene products using BLASTP (available on the internet site“blast.ncbi.nlm.nih.gov/Blast.cgi”) against the UniProt database(available on the world wide web internet site “ uniprot.org/”). Genespresent in individual genomes of NLS0017, NLS0020, NLS0037, NLS0042,NLS0065, and NLS0066 that could improve lettuce production (as shown inExample 7) but absent in the whole set of genomes of NLS0135, NLS0071,NLS0109, and NLS0142 that did not improve lettuce production (as shownin Example 7) were identified in OrthoMCL clusters using customsoftware. The encoded proteins found in the Methylobacterium NLS0017,NLS0020, NLS0037, NLS0042, NLS0065, and NLS0066 that could improvelettuce production are provided in the sequencing listing as SEQ ID NO:1-5125. The nucleic acid sequences that encode the proteins of SEQ IDNO: 1-5125 are SEQ ID NO: 5126-10250, respectively. The proteins encodedby genes present in NLS0017 but absent from NLS0135, NLS0071, NLS0109,and NLS0142 are provided as SEQ ID NO: 1-1086. The proteins encoded bygenes present in NLS0020 but absent from NLS0135, NLS0071, NLS0109, andNLS0142 are provided as SEQ ID NO: 1087-2176. The proteins encoded bygenes present in NLS0037 but absent from NLS0135, NLS0071, NLS0109, andNLS0142 are provided as SEQ ID NO: 2177-2461. The proteins encoded bygenes present in NLS0042 but absent from NLS0135, NLS0071, NLS0109, andNLS0142 are provided as SEQ ID NO: 2462-3347. The proteins encoded bygenes present in NLS0065 but absent from NLS0135, NLS0071, NLS0109, andNLS0142 are provided as SEQ ID NO: 3348-3949. The proteins encoded bygenes present in NLS0066 but absent from NLS0135, NLS0071, NLS0109, andNLS0142 are provided as SEQ ID NO: 3950-5125. Orthologous gene groupsrepresenting genes encoding proteins found in the genomes of at leasttwo individual genomes of NLS0017, NLS0020, NLS0037, NLS0042, NLS0065,and/or NLS0066 that could improve lettuce production (as shown inExample 7) but that are absent in the whole set of genomes of NLS0135,NLS0071, NLS0109, and NLS0142 that did not improve lettuce productionare provided in Table 7. In Table 7, groups of orthologous genes areprovided in each row, where the longest sequence and associated uniqueSeq ID Number are designated as a reference sequence to represent theortholog cluster (Column 3 of Table 7). The ortholog groupidentification number is provided in column 1 of Table 7, the closestgene identity based on database comparisons is provided in column 2 ofTable 7, and the reference sequence for each ortholog cluster isprovided in column 3 of Table 7. Examples of ortholog sequences found inNLS0017, NLS0020, NLS0037, NLS0042, NLS0065, and NLS0066 are provided asSEQ ID NO: in Table 7, columns 4, 5, 6, 7, 8, and 9, respectively.

TABLE 7 Orthologous Gene Groups Reference. NLS0017 NLS0020 NLS0037NLS0042 NLS0065 NLS0066 Unique Ortholog Ortholog Ortholog OrthologOrtholog Ortholog Ortholog Ortholog Group SEQ ID SEQ ID SEQ ID SEQ IDSEQ ID SEQ ID SEQ ID Identifier Annotation NO: NO: NO: NO: NO: NO: NO:4678v20141116 hypothetical protein 2467 8 1091 NA 2467 3352 3954Mpop_4447 4682v20141116 hypothetical protein 2468 9 1092 NA 2468 33533955 Mchl_0132 4747v20141116 histidine kinase 3357 11 1093 NA 2472 33573959 4748v20141116 transcriptional 1094 12 1094 NA 2473 3358 3960regulator 4749v20141116 histidine kinase 13 13 1095 NA 2474 3359 39614809v20141116 saccharopine 14 14 1097 NA 2481 3365 3966 dehydrogenase4837v20141116 ABC transporter-like 1100 17 1100 2179 2484 3367 NAprotein 4841v20141116 hypothetical protein 3968 19 1102 NA 2486 33683968 Mpop_0734 4904v20141116 HlyD family type I 3370 22 1103 NA 24913370 3972 secretion membrane fusion protein 4905v20141116Transcriptional 23 23 1104 NA 2492 3371 3973 regulator XRE family4942v20141116 type I secretion system 1106 25 1106 NA 2494 3373 3974ATPase 3799v20141116 hypothetical protein 3950 1 1088 NA 2462 NA 39504369v20141116 hypothetical protein 3952 6 1090 2177 NA NA 3952 METDI00484454v20141116 FAD-dependent 2463 7 NA 2178 2463 3348 NA pyridinenucleotide- disulfide oxidoreductase 4740v20141116 arsenite efflux pump2471 10 NA NA 2471 3356 3958 ACR3 4926v20141116 LysR family 3372 24 1105NA 2493 3372 NA transcriptional regulator 4948v20141116 hypotheticalprotein 2180 26 NA 2180 2495 3374 NA Mchl_1383 5012v20141116 COG3293:Transposase 27 27 1107 NA 2500 3377 NA and inactivated derivatives5041v20141116 hypothetical protein 28 28 1108 NA 2502 3378 NA5096v20141116 hypothetical protein 30 30 1109 NA 2504 3380 NA5122v20141116 hypothetical protein 2510 31 1110 NA 2510 3385 NAMchl_3038 5202v20141116 hypothetical protein 2515 33 1113 NA 2515 3387NA Mext_4122 5212v20141116 hypothetical protein 1114 35 1114 NA 25163388 NA 5238v20141116 OmpA/MotB domain- 3987 36 1115 NA NA 3392 3987containing protein 5246v20141116 multidrug transporter 1116 37 1116 21822521 NA NA MatE 5258v20141116 hypothetical protein 1117 38 1117 NA 25223393 NA 5263v20141116 porin 3394 39 1118 NA 2523 3394 NA 5363v20141116hypothetical protein 40 40 1119 NA 2533 3401 NA 5374v20141116 cytochromeP450 1120 41 1120 NA 2534 NA 3992 5433v20141116 peptidase C14 3996 421121 NA NA 3412 3996 5434v20141116 hypothetical protein 43 43 1122 NA NA3413 3997 5497v20141116 ATPase 44 44 NA NA 2561 3425 4003 5506v20141116hypothetical protein 4004 45 1123 NA NA 3426 4004 5507v20141116hypothetical protein 3427 46 1124 NA NA 3427 4005 5508v20141116hypothetical protein 4006 47 1125 NA NA 3428 4006 Mpop_07255509v20141116 hypothetical protein 3429 48 1126 NA NA 3429 40075510v20141116 hypothetical protein 3430 49 1127 NA NA 3430 40085585v20141116 hypothetical protein 51 51 1128 NA NA 3443 4012 Mpop_07225586v20141116 hypothetical protein 52 52 1129 NA NA 3444 4013 Mpop_07235790v20141116 hypothetical protein 57 57 1134 NA 2619 3476 NA5984v20141116 Penicillin-binding 2676 60 1136 NA 2676 3502 NA protein6022v20141116 plasmid stabilization 2190 NA 1139 2190 2680 NA 4021protein ParE 6819v20141116 short-chain 76 76 1155 2201 NA 3542 NAdehydrogenase 7006v20141116 binding-protein- 4067 84 1163 NA 2796 NA4067 dependent transport system inner membrane protein 7040v20141116hypothetical protein 85 85 1164 NA 2799 NA 4069 7299v20141116glycosyltransferase 1180 105 1180 2206 NA NA 4087 family 2 7707v20141116metal-dependent 127 127 1203 2214 NA NA 4111 phosphohydrolase8313v20141116 GDP-L-fucose synthase 197 197 1264 2237 NA NA 41718314v20141116 NAD-dependent 198 198 1265 2238 NA NA 4172epimerase/dehydratase 8315v20141116 NAD-dependent 199 199 1266 2239 NANA 4173 epimerase/dehydratase 8898v20141116 Transcriptional 2971 2501309 2263 2971 NA NA regulator LysR family 4353v20141116 transposasepartial 5 5 1089 NA NA NA 3951 4597v20141116 peroxiredoxin 2464 NA NA NA2464 3350 3953 4733v20141116 acyl-CoA 3956 NA NA NA 2469 3354 3956dehydrogenase type 2 domain 4734v20141116 ABC transporter 3355 NA NA NA2470 3355 3957 4782v20141116 ABC transporter inner 2475 NA NA NA 24753360 3962 membrane protein 4783v20141116 twin-arginine 2476 NA NA NA2476 3361 3963 translocation pathway signal 4792v20141116 COG3293:Transposase 1096 NA 1096 NA 2477 3362 NA and inactivated derivatives4797v20141116 hypothetical protein 3364 NA NA NA 2480 3364 3964METDI2339 4829v20141116 diguanylate cyclase 3366 NA NA NA 2482 3366 39674831v20141116 Hypothetical protein 16 16 1098 NA 2483 NA NA4839v20141116 hypothetical protein 2485 18 1101 NA 2485 NA NA4901v20141116 OmpW family protein 3971 NA NA NA 2490 3369 39715103v20141116 hypothetical protein 3381 NA NA NA 2506 3381 3977METDI2906 5118v20141116 aminoglycoside 2508 NA NA NA 2508 3383 3978phosphotransferase 5144v20141116 hypothetical protein 1111 NA 1111 2181NA NA 3980 5183v20141116 ABC transporter 2513 32 1112 NA 2513 NA NA5217v20141116 hemolysin 2517 NA NA NA 2517 3389 3985 5283v20141116BadM/Rrf2 family 3988 NA NA NA 2525 3396 3988 transcriptional regulator5391v20141116 5′-nucleotidase 2543 NA NA NA 2543 3407 3994 5420v20141116virulence-associated 3411 NA NA NA 2547 3411 3995 protein D5471v20141116 hypothetical protein 3416 NA NA NA 2550 3416 3998Mpop_1169 5473v20141116 hypothetical protein 2551 NA NA NA 2551 34173999 Mpop_3884 5487v20141116 hypothetical protein 2558 NA NA NA 25583422 4002 5513v20141116 hypothetical protein 3431 50 NA NA 2563 3431 NAMext_2210 5566v20141116 hypothetical protein 4010 NA NA NA 2572 34394010 METDI0649 5669v20141116 hypothetical protein 53 53 1130 NA NA 3458NA 5675v20141116 GreA/GreB family 54 54 1131 NA NA 3460 NA elongationfactor 5683v20141116 RND family efflux 2590 NA NA 2183 2590 3462 NAtransporter MFP subunit 5728v20141116 permease of ABC 2603 NA NA 21842603 NA 4016 transporter 5782v20141116 hypothetical protein 2617 56 NANA 2617 3474 NA METDI1995 5850v20141116 hypothetical protein 4018 NA NANA 2631 3485 4018 5911v20141116 hypothetical protein 2647 NA NA NA 26473497 4019 MexAM1_META1p1120 5989v20141116 hypothetical protein 61 611137 NA 2677 NA NA 6009v20141116 TetR family 1138 62 1138 NA 2679 NA NAtranscriptional regulator 6028v20141116 UDP-glucose 6- 63 63 1140 NA NA3504 NA dehydrogenase 6091v20141116 DNA topoisomerase III 64 64 1141 NANA NA 4024 6093v20141116 Fe—S type 65 65 1142 NA NA NA 4025tartrate/fumarate subfamily hydro-lyase subunit alpha 6183v20141116PAS/PAC sensor hybrid 2697 NA NA NA 2697 3513 4028 histidine kinase6196v20141116 hypothetical protein 67 67 NA 2191 2700 NA NA6235v20141116 hypothetical protein 1144 70 1144 NA NA NA 40316301v20141116 hypothetical protein 2709 NA NA NA 2709 3517 4032Mchl_1527 6437v20141116 Sel1 domain- 3521 72 1146 NA NA 3521 NAcontaining protein 6442v20141116 fumarate hydratase 2724 73 1147 NA 2724NA NA 6618v20141116 hypothetical protein 2745 NA NA 2199 2745 NA 4045Mpop_4203 6687v20141116 peptide ABC 75 75 1152 NA NA 3534 NA transportersubstrate- binding protein 6785v20141116 hydrolase alpha/beta 2763 NA NANA 2763 3540 4052 hydrolase fold family protein 6823v20141116thioesterase 77 77 1157 NA NA 3543 NA superfamily protein 7042v20141116arginine ABC 86 86 1165 NA NA NA 4070 transporter ATP- binding protein7043v20141116 glyoxalase/bleomycin 2800 87 1166 NA 2800 NA NA resistanceprotein/dioxygenase 7048v20141116 glyoxalase 89 89 1167 NA NA NA 40717189v20141116 hypothetical protein 1172 97 1172 NA NA NA 4077VOLCADRAFT_119358 7290v20141116 succinate 4080 98 1173 NA NA NA 4080dehydrogenase and fumarate reductase iron-sulfur protein 7291v20141116succinate 99 99 1174 NA NA NA 4081 dehydrogenase membrane anchor7292v20141116 succinate 100 100 1175 NA NA NA 4082 dehydrogenasecytochrome b subunit 7293v20141116 L(+)-tartrate or 101 101 1176 NA NANA 4083 fumarate dehydratase subunit beta 7294v20141116 fumaratereductase 102 102 1177 NA NA NA 4084 7295v20141116 YCII-like protein 103103 1178 NA NA NA 4085 7297v20141116 TRAP-type transport 104 104 1179 NANA NA 4086 system periplasmic component-like protein 7310v20141116 ABCtransporter 4088 106 1183 NA NA NA 4088 substrate-binding protein7311v20141116 glutathione ABC 107 107 1184 NA NA NA 4089 transporterpermease GsiD 7312v20141116 oligopeptide/dipeptide 1185 108 1185 NA NANA 4090 ABC transporter ATPase 7313v20141116 ABC transporter-like 109109 1186 NA NA NA 4091 protein 7338v20141116 acyl-CoA 113 113 1188 2208NA NA NA dehydrogenase domain-containing protein 7341v20141116hypothetical protein 4094 114 1189 NA NA NA 4094 M446_1279 7508v20141116hypothetical protein 2856 NA 1193 NA 2856 NA 4104 7536v20141116FAD-binding 121 121 1194 NA NA 3583 NA monooxygenase 7711v201411162-hydroxyacid 4112 128 1204 NA NA NA 4112 dehydrogenase 7729v20141116amino acid ABC 4113 130 1206 NA NA NA 4113 transporter 7730v20141116GntR family 131 131 1207 NA NA NA 4114 transcriptional regulator7750v20141116 alpha-amylase 135 135 1209 NA NA NA 4115 7844v20141116hypothetical protein 139 139 1214 NA 2890 NA NA 7845v20141116FAD-dependent 2216 140 1215 2216 NA NA NA oxidoreductase 7868v20141116hypothetical protein 143 143 1217 NA NA NA 4126 7877v20141116hypothetical protein 4127 145 1220 NA NA NA 4127 Mchl_0532 7885v20141116binding-protein- 146 146 1221 NA NA NA 4128 dependent transport systeminner membrane protein 7890v20141116 taurine ABC 1223 148 1223 NA NA NA4129 transporter permease 7907v20141116 regulator 3602 151 1225 NA NA3602 NA 7912v20141116 Asp/Glu/hydantoin 1226 153 1226 2218 NA NA NAracemase 7913v20141116 D-lactate 154 154 1227 NA NA NA 4130dehydrogenase 8031v20141116 hypothetical protein 155 155 1231 2221 NA NANA 8053v20141116 acetyltransferase 158 158 1234 NA NA NA 41438056v20141116 amidohydrolase 159 159 1235 2222 NA NA NA 8057v20141116ABC transporter 160 160 1236 2223 NA NA NA 8058v20141116 ABC transporter161 161 1237 2224 NA NA NA permease 8059v20141116 putative ABC 162 1621238 2225 NA NA NA transporter periplasmic substrate- binding protein8080v20141116 hypothetical protein 163 163 1239 NA NA NA 41458083v20141116 N-ethylammeline 164 164 1240 2226 NA NA NA chlorohydrolase8084v20141116 hydantoin racemase 165 165 1241 2227 NA NA NA8095v20141116 glucose-methanol- 2228 169 1242 2228 NA NA NA cholineoxidoreductase 8099v20141116 Asp/Glu/hydantoin 2229 172 1244 2229 NA NANA racemase 8114v20141116 polysaccharide 175 175 1245 NA NA NA 4150deacetylase 8273v20141116 ABC transporter 2234 186 1255 2234 NA NA NApermease 8289v20141116 hypothetical protein 2235 188 1257 2235 NA NA NA8300v20141116 Holliday junction DNA 191 191 1259 NA NA NA 4168 helicaseRuvB 8303v20141116 amidase 1260 193 1260 2236 NA NA NA 8310v20141116monooxygenase 195 195 1262 NA NA NA 4170 8318v20141116 hypotheticalprotein 200 200 1267 NA NA NA 4174 8331v20141116 hypothetical protein202 202 1268 NA NA NA 4175 8335v20141116 hypothetical protein 4176 2051271 NA NA NA 4176 8475v20141116 hypothetical protein 210 210 1276 2249NA NA NA 8524v20141116 oxidoreductase 215 215 1280 NA NA NA 41908538v20141116 dehydrogenase 218 218 1283 2250 NA NA NA 8539v20141116AraC family 2251 219 1284 2251 NA NA NA transcriptional regulator8573v20141116 alkanal 221 221 1286 NA NA NA 4191 monooxygenase8579v20141116 hypothetical protein 223 223 1287 NA NA NA 41928592v20141116 hydroxymethylglutaryl- 226 226 1289 2255 NA NA NA CoAlyase 8593v20141116 hypothetical protein 3631 227 1290 NA NA 3631 NA8599v20141116 hypothetical protein 2939 229 1292 NA 2939 NA NA8603v20141116 GntR family 232 232 1294 2256 NA NA NA transcriptionalregulator 8642v20141116 binding-protein- 235 235 1297 2257 NA NA NAdependent transport system inner membrane protein 8643v20141116 ABCtransporter 2258 236 1298 2258 NA NA NA permease 8644v20141116 ABCtransporter 237 237 1299 2259 NA NA NA substrate-binding protein8867v20141116 hypothetical protein 244 244 1305 NA 2969 NA NA8906v20141116 methylcrotonoyl-CoA 254 254 1312 2265 NA NA NA carboxylase8907v20141116 TetR family 2266 255 1313 2266 NA NA NA transcriptionalregulator 8922v20141116 response regulator 4206 257 1315 NA NA NA 4206receiver protein 8932v20141116 transthyretin 266 266 1319 2267 NA NA NA8957v20141116 hypothetical protein 274 274 1327 NA NA 3647 NA9274v20141116 hypothetical protein 2278 291 1350 2278 NA NA NAMrad2831_4275 9275v20141116 3-methylcrotonyl-CoA 2279 292 1351 2279 NANA NA carboxylase subunit alpha 9277v20141116 transposase 293 293 1352NA NA NA 4244 9280v20141116 glycosyltransferase 2990 295 1354 NA 2990 NANA 9320v20141116 hydrolase 314 314 1365 2283 NA NA NA 9324v20141116hypothetical protein 316 316 1367 NA NA 3664 NA 9342v20141116hypothetical protein 2284 NA 1372 2284 NA 3665 NA 9755v20141116hypothetical protein 362 362 1419 2290 NA NA NA 9774v20141116 ATPase1424 374 1424 NA NA 3678 NA 9781v20141116 UDP- 2292 376 1426 2292 NA NANA glucosyltransferase 10245v20141116 acetolactate synthase 393 393 14482303 NA NA NA 10246v20141116 GntR family 2304 394 1449 2304 NA NA NAtranscriptional regulator 10263v20141116 hypothetical protein 409 4091463 2305 NA NA NA 10329v20141116 fatty acid--CoA ligase 456 456 15072309 NA NA NA 10348v20141116 None 469 469 1517 NA NA 3694 NA11120v20141116 hypothetical protein 577 577 1629 2319 NA NA NA15411v20141116 NAD-binding 6- 925 925 2062 2369 NA NA NAphosphogluconate dehydrogenase 4672v20141116 heme peroxidase with 3351NA NA NA 2466 3351 NA hemolysin-type calcium-binding domain4897v20141116 elongation factor Tu 2489 NA NA NA 2489 NA 39705002v20141116 thiol-disulfide 2498 NA NA NA 2498 3375 NA oxidoreductase5040v20141116 AraC family 2501 NA NA NA 2501 NA 3976 transcriptionalregulator 5079v20141116 flagellar hook-length 3379 NA NA NA 2503 3379 NAcontrol protein 5117v20141116 hypothetical protein 3382 NA NA NA 25073382 NA 5119v20141116 multidrug ABC 3384 NA NA NA 2509 3384 NAtransporter ATP- binding protein 5147v20141116 hypothetical protein 2511NA NA NA 2511 NA 3981 Mpop_1464 5180v20141116 glycoside hydrolase 3386NA NA NA 2512 3386 NA family 3 5184v20141116 hypothetical protein 2514NA NA NA 2514 NA 3982 5205v20141116 DNA invertase gene 34 34 NA NA NA NA3984 rlgA 5219v20141116 hypothetical protein 3986 NA NA NA 2518 NA 3986MexAM1_META1p0208 5228v20141116 ABC transporter 3390 NA NA NA 2519 3390NA permease 5233v20141116 membrane protein 3391 NA NA NA 2520 3391 NA5275v20141116 gamma- 2524 NA NA NA 2524 3395 NA glutamyltransferase5284v20141116 hypothetical protein 2526 NA NA NA 2526 3397 NAMexAM1_META1p3378 5287v20141116 FAD linked oxidase 2527 NA NA NA 25273398 NA domain-containing protein 5289v20141116 Siderophore 2528 NA NANA 2528 3399 NA synthetase component 5318v20141116 hypothetical protein2529 NA NA NA 2529 NA 3989 Mpop_4361 5335v20141116 AraC family 3990 NANA NA 2531 NA 3990 transcriptional regulator 5337v20141116 hypotheticalprotein 2532 NA NA NA 2532 3400 NA Mpop_4929 5379v20141116 hypotheticalprotein 2535 NA NA NA 2535 3402 NA MexAM1_META1p2104 5381v201411164Fe—4S ferredoxin 3403 NA NA NA 2537 3403 NA 5382v20141116 hypotheticalprotein 3404 NA NA NA 2538 3404 NA METDI4726 5383v20141116 hypotheticalprotein 2539 NA NA NA 2539 3405 NA Mext_3764 5384v20141116N-acetyltransferase 3406 NA NA NA 2540 3406 NA GCN5 5390v20141116hypothetical protein 3993 NA NA NA 2541 NA 3993 5392v20141116hypothetical protein 3408 NA NA NA 2544 3408 NA Mext_3467 5398v20141116hypothetical protein 2545 NA NA NA 2545 3409 NA Mchl_3886 5419v20141116diguanylate cyclase 3410 NA NA NA 2546 3410 NA 5437v20141116hypothetical protein 2548 NA NA NA 2548 3414 NA Mpop_2189 5466v20141116hypothetical protein 2549 NA NA NA 2549 3415 NA Mpop_0206 5475v20141116conserved hypothetical 2552 NA NA NA 2552 NA 4000 protein 5476v20141116hypothetical protein 4001 NA NA NA 2553 NA 4001 AZOLI_p403795477v20141116 HAD-superfamily 2554 NA NA NA 2554 3418 NA hydrolase5480v20141116 hypothetical protein 3419 NA NA NA 2555 3419 NA METDI42615482v20141116 hypothetical protein 2556 NA NA NA 2556 3420 NAMexAM1_META1p3862 5483v20141116 hypothetical protein 3421 NA NA NA 25573421 NA 5488v20141116 fatty acid desaturase; 2559 NA NA NA 2559 3423 NAmembrane protein 5490v20141116 hypothetical protein 2560 NA NA NA 25603424 NA MexAM1_META1p1300 5524v20141116 hypothetical protein 3432 NA NANA 2564 3432 NA 5525v20141116 hypothetical protein 2565 NA NA NA 25653433 NA Mpop_5158 5526v20141116 hypothetical protein 2566 NA NA NA 25663434 NA Mext_4623 5530v20141116 Bacterial extracellular 4009 NA NA NA2567 NA 4009 solute-binding protein family 3 5536v20141116 hypotheticalprotein 2568 NA NA NA 2568 3435 NA 5543v20141116 xylose isomerase 2569NA NA NA 2569 3436 NA domain-containing protein 5546v20141116hypothetical protein 3437 NA NA NA 2570 3437 NA MexAM1_META1p04835556v20141116 diguanylate cyclase 3438 NA NA NA 2571 3438 NA5568v20141116 protein transcription 3440 NA NA NA NA 3440 4011 factor5577v20141116 hypothetical protein 2573 NA NA NA 2573 3441 NA Mpop_15615578v20141116 sodium:solute 2574 NA NA NA 2574 3442 NA symporter5610v20141116 hypothetical protein 2575 NA NA NA 2575 3445 NA Mchl_23925612v20141116 hypothetical protein 2576 NA NA NA 2576 3446 NAMexAM1_META1p5060 5618v20141116 hypothetical protein 3447 NA NA NA 25773447 NA 5619v20141116 hypothetical protein 3448 NA NA NA 2578 3448 NAMexAM1_META1p2965 5625v20141116 hypothetical protein 2580 NA NA NA 25803449 NA Mchl_4383 5626v20141116 hypothetical protein 3450 NA NA NA 25813450 NA Mext_3503 5627v20141116 protein-L-isoaspartate 2582 NA NA NA2582 3451 NA O-methyltransferase 5628v20141116 hypothetical protein 2583NA NA NA 2583 3452 NA 5635v20141116 hypothetical protein 2584 NA NA NA2584 3453 NA Mext_4188 5636v20141116 hypothetical protein 2585 NA NA NA2585 3454 NA Mpop_4705 5642v20141116 hypothetical protein 4014 NA NA NANA 3455 4014 METDI0650 5650v20141116 ATPase 2586 NA NA NA 2586 3456 NA5657v20141116 two component LuxR 2587 NA NA NA 2587 3457 NA familytranscriptional regulator 5672v20141116 hypothetical protein 2588 NA NANA 2588 3459 NA MexAM1_META1p1076 5679v20141116 acetate kinase 2589 NANA NA 2589 3461 NA 5684v20141116 hypothetical protein 2591 NA NA NA 2591NA 4015 5686v20141116 EAL domain-containing 2592 NA NA NA 2592 3463 NAprotein 5689v20141116 AsnC family 2593 NA NA NA 2593 3464 NAtranscriptional regulator 5691v20141116 hypothetical protein 2594 NA NANA 2594 3465 NA Mchl_3961 5692v20141116 two-component LuxR 2595 NA NA NA2595 3466 NA family transcriptional regulator 5693v20141116 hypotheticalprotein 2596 NA NA NA 2596 3467 NA Mpop_0877 5695v20141116 secretionprotein HlyD 2598 NA NA NA 2598 3468 NA 5698v20141116 hypotheticalprotein 3469 NA NA NA 2599 3469 NA Mext_0717 5699v20141116transcriptional 2600 NA NA NA 2600 3470 NA regulator 5712v20141116 HlyDfamily type I 2602 NA NA NA 2602 3471 NA secretion membrane fusionprotein 5735v20141116 integrase catalytic 55 55 1132 NA NA NA NA subunit5737v20141116 putative transposase 2185 NA 1133 2185 NA NA NA5745v20141116 hypothetical protein 4017 NA NA NA 2606 NA 4017 Mpop_00655752v20141116 hypothetical protein 2610 NA NA NA 2610 3472 NA Mpop_08585756v20141116 hypothetical protein 2612 NA NA NA 2612 3473 NA Mext_11915783v20141116 rhizobiocin secretion 2618 NA NA NA 2618 3475 NA proteinrspD 5802v20141116 hypothetical protein 3477 NA NA NA 2620 3477 NAMext_3619 5803v20141116 NADP-dependent 2621 NA NA NA 2621 3478 NAalcohol dehydrogenase 5812v20141116 Urease accessory 2625 NA NA NA 26253479 NA protein UreD 5813v20141116 urea transporter 2626 NA NA NA 26263480 NA 5814v20141116 ammonium 2627 NA NA NA 2627 3481 NA transporter5822v20141116 hypothetical protein 2628 NA NA NA 2628 3482 NAMexAM1_META1p3379 5845v20141116 hypothetical protein 2630 NA NA 21862630 NA NA Mpop_0716 5859v20141116 hemolysin-type 3486 NA NA NA 26323486 NA calcium-binding protein 5866v20141116 hypothetical protein 3487NA NA NA 2633 3487 NA Mchl_1323 5872v20141116 hypothetical protein 2636NA NA NA 2636 3488 NA Mpop_3121 5881v20141116 hypothetical protein 2187NA NA 2187 2638 NA NA Mpop_1945 5884v20141116 urease subunit gamma 3489NA NA NA 2640 3489 NA 5885v20141116 urease subunit beta 2641 NA NA NA2641 3490 NA 5886v20141116 camphor resistance 2642 NA NA NA 2642 3491 NAprotein CrcB 5887v20141116 UreE urease accessory 3492 NA NA NA 2643 3492NA domain-containing protein 5888v20141116 urease accessory 2644 NA NANA 2644 3493 NA protein UreF 5889v20141116 urease accessory 3494 NA NANA 2645 3494 NA protein UreG 5890v20141116 hypothetical protein 3495 NANA NA 2646 3495 NA 5934v20141116 carbon monoxide 58 58 1135 NA NA NA NAdehydrogenase subunit G 5937v20141116 hypothetical protein 59 59 NA NA2662 NA NA 5952v20141116 nucleotidyltransferase 4020 NA NA NA 2664 NA4020 5958v20141116 hypothetical protein 3498 NA NA NA 2668 3498 NAMpop_2489 5963v20141116 camphor resistance 3499 NA NA NA 2670 3499 NACrcB protein 5964v20141116 acid-resistance protein 2671 NA NA NA 26713500 NA 5970v20141116 hypothetical protein 3501 NA NA NA 2672 3501 NA5976v20141116 hypothetical protein 2188 NA NA 2188 2673 NA NA Mext_21986008v20141116 chloride channel 2678 NA NA NA 2678 3503 NA protein6037v20141116 hypothetical protein 2681 NA NA NA 2681 NA 4022 Mext_20296040v20141116 diguanylate cyclase 2682 NA NA NA 2682 3505 NA6045v20141116 hypothetical protein 3506 NA NA NA NA 3506 4023 Mpop_38796100v20141116 N-acetyltransferase 2684 NA NA NA 2684 3507 NA GCN56123v20141116 TetR family 66 66 1143 NA NA NA NA transcriptionalregulator 6155v20141116 hypothetical protein 3508 NA NA NA 2690 3508 NAMext_0184 6156v20141116 hypothetical protein 2691 NA NA NA 2691 3509 NAMexAM1_META1p2841 6179v20141116 hypothetical protein 2694 NA NA NA 26943510 NA METDI1994 6180v20141116 oleate hydratase 2695 NA NA NA 2695 3511NA 6182v20141116 hypothetical protein 2696 NA NA NA 2696 3512 NAMext_4657 6187v20141116 hypothetical protein 2699 NA NA NA 2699 NA 4029Mpop_4217 6198v20141116 hypothetical protein 2701 NA NA NA 2701 NA 4030Mchl_4111 6211v20141116 LysR family 2702 69 NA NA 2702 NA NAtranscriptional regulator 6228v20141116 MucR family 2704 NA NA NA 27043514 NA transcriptional regulator 6266v20141116 hypothetical protein2707 NA NA NA 2707 3515 NA Mpop_4875 6267v20141116 hypothetical protein2708 NA NA NA 2708 3516 NA Mpop_0711 6302v20141116 hypothetical protein2710 NA NA NA 2710 3518 NA Mext_4665 6316v20141116 hypothetical protein1145 71 1145 NA NA NA NA 6323v20141116 hypothetical protein 2712 NA NANA 2712 NA 4034 Mchl_1272 6355v20141116 hypothetical protein 2713 NA NA2192 2713 NA NA MexAM1_META1p2729 6403v20141116 hypothetical protein4036 NA NA 2194 NA NA 4036 6404v20141116 hypothetical protein 4037 NA NA2195 NA NA 4037 6405v20141116 hypothetical protein 2196 NA NA 2196 NA NA4038 6409v20141116 hypothetical protein 3519 NA NA NA 2718 3519 NA6410v20141116 putative 2 4 3520 NA NA NA 2719 3520 NAdihydroxyhept-2-ene-l 7-dioic acid aldolase 6412v20141116 amidohydrolase2720 NA NA NA 2720 NA 4039 6451v20141116 integrase family 74 74 NA NA NA3522 NA protein 6472v20141116 hypothetical protein 2197 NA 1148 2197 NANA NA FBFL15_0362 6475v20141116 hypothetical protein 3523 NA 1149 NA NA3523 NA 6566v20141116 hypothetical protein 2738 NA NA NA 2738 NA 4040Mchl_1240 6568v20141116 hypothetical protein 2740 NA NA NA 2740 NA 4041Mchl_4341 6571v20141116 hypothetical protein 3524 NA NA NA NA 3524 4042MexAM1_META1p4650 6576v20141116 hypothetical protein 2741 NA NA NA 2741NA 4043 6587v20141116 hypothetical protein 3525 NA NA NA 2743 3525 NAMETDI5212 6615v20141116 hypothetical protein 1151 NA 1151 NA NA 3526 NA6616v20141116 hypothetical protein 3527 NA NA NA NA 3527 40446649v20141116 hypothetical protein 2748 NA NA NA 2748 3530 NA6655v20141116 hypothetical protein 3531 NA NA NA 2751 3531 NA6656v20141116 hypothetical protein 2753 NA NA NA 2753 3532 NA Mext_08086665v20141116 hypothetical protein 2754 NA NA NA 2754 NA 40486670v20141116 ubiE/COQ5 2756 NA NA NA 2756 3533 NA methyltransferasefamily enzyme 6713v20141116 cytochrome C 3535 NA NA NA NA 3535 4049biogenesis protein CcsA 6749v20141116 hypothetical protein 1153 NA 1153NA NA 3537 NA 6750v20141116 hypothetical protein 1154 NA 1154 NA NA 3538NA 6777v20141116 hypothetical protein 2200 NA NA 2200 NA NA 40516778v20141116 choloylglycine 3539 NA NA NA 2759 3539 NA hydrolase6824v20141116 transposase of ISMex3 78 78 1158 NA NA NA NA IS256 family6829v20141116 hypothetical protein 2765 NA NA NA 2765 3544 NA6832v20141116 HEPN domain- 4055 NA NA NA 2766 NA 4055 containing protein6833v20141116 regulatory protein LysR 3546 NA NA NA 2767 3546 NA6835v20141116 hypothetical protein 2202 NA NA 2202 NA NA 4056 Mchl_55536876v20141116 fermentative D-lactate 2774 NA NA NA 2774 3553 NAdehydrogenase NAD- dependent 6881v20141116 hypothetical protein 2777 NANA NA 2777 NA 4057 6892v20141116 hypothetical protein 2778 NA NA NA 2778NA 4059 6923v20141116 Hypothetical protein 1159 82 1159 NA NA NA NA6941v20141116 hypothetical protein 2779 83 NA NA 2779 NA NA Mext_11236946v20141116 hypothetical protein 1161 NA 1161 NA NA NA 40616982v20141116 hypothetical protein 2790 NA NA NA 2790 3558 NA Mext_13277002v20141116 esterase 2794 NA NA NA 2794 3559 NA 7004v20141116hypothetical protein 2795 NA NA NA 2795 NA 4065 Mpop_1856 7028v20141116hypothetical protein 2797 NA NA NA 2797 NA 4068 7057v20141116hypothetical protein 3560 NA 1169 NA NA 3560 NA 7068v20141116 xyloseisomerase 2801 NA NA NA 2801 NA 4072 domain-containing protein7077v20141116 NADPH-dependent 2203 NA NA 2203 2802 NA NA FMN reductase7083v20141116 glutathione S- 2204 NA NA 2204 NA NA 4073 transferase7096v20141116 diguanylate cyclase 2808 NA NA NA 2808 3563 NA7116v20141116 transposase mutator 1170 90 1170 NA NA NA NA type7127v20141116 hypothetical protein 4074 94 NA NA NA NA 4074 Mnod_69857149v20141116 hypothetical protein 4075 NA NA NA NA 3564 40757158v20141116 short-chain 3565 NA NA NA 2816 3565 NAdehydrogenase/reductase SDR 7238v20141116 methyl-accepting 4078 NA NA NANA 3568 4078 chemotaxis sensory transducer 7242v20141116 flagellar hooklength 2817 NA NA NA 2817 3570 NA determination protein 7272v20141116hypothetical protein 4079 NA NA NA 2823 NA 4079 MexAM1_META1p08877303v20141116 glycosyl hydrolase 2827 NA 1182 NA 2827 NA NA7316v20141116 hypothetical protein 4092 NA NA 2207 NA NA 4092 Mpop_44117318v20141116 hypothetical protein 110 110 1187 NA NA NA NAMrad2831_3608 7330v20141116 short-chain 2831 NA NA NA 2831 NA 4093dehydrogenase/reductase SDR 7334v20141116 hypothetical protein 112 112NA NA 2832 NA NA 7364v20141116 IclR family 2833 NA NA NA 2833 NA 4095transcriptional regulator 7384v20141116 hypothetical protein 4096 NA NANA NA 3576 4096 Mpop_4088 7388v20141116 hypothetical protein 2834 NA NANA 2834 NA 4097 Mpop_4204 7389v20141116 peptidase M24 2835 NA NA NA 2835NA 4098 7390v20141116 thiamine 2836 NA NA NA 2836 NA 4099 pyrophosphateprotein central region 7399v20141116 hypothetical protein 3577 NA NA NA2842 3577 NA 7418v20141116 hypothetical protein 2209 NA NA 2209 2843 NANA 7420v20141116 hypothetical protein 2844 NA NA NA 2844 3578 NAMchl_5174 7422v20141116 hypothetical protein 2845 NA NA NA 2845 3579 NAMext_4882 7435v20141116 hypothetical protein 2852 NA NA NA 2852 NA 41017437v20141116 hypothetical protein 4102 NA NA NA NA 3581 4102LILAB_22195 7465v20141116 hypothetical protein 3582 NA NA 2210 NA 3582NA 7482v20141116 phage putative protein 1190 117 1190 NA NA NA NA7484v20141116 hypothetical protein 119 119 1191 NA NA NA NA7489v20141116 enoyl-CoA 120 120 1192 NA NA NA NA hydratase/isomerase7517v20141116 inner-membrane 2857 NA NA NA 2857 NA 4105 translocator7518v20141116 branched chain amino 4106 NA NA NA 2858 NA 4106 acid ABCtransporter substrate-binding protein 7558v20141116 hypothetical protein3584 NA 1195 NA NA 3584 NA 7562v20141116 integrase catalytic 123 1231196 NA NA NA NA subunit 7586v20141116 hypothetical protein 3586 NA 1198NA NA 3586 NA 7587v20141116 hypothetical protein 3587 NA 1199 NA NA 3587NA 7588v20141116 hypothetical protein 1200 NA 1200 NA NA 3588 NA7589v20141116 hypothetical protein 1201 NA 1201 NA NA 3589 NA7590v20141116 hypothetical protein 2211 NA NA 2211 NA NA 4107Mrad2831_2637 7624v20141116 N-acetyltransferase 2212 NA NA 2212 2861 NANA GCN5 7699v20141116 hypothetical protein 126 126 1202 NA NA NA NA7713v20141116 hypothetical protein 129 129 1205 NA NA NA NA7734v20141116 hypothetical protein 2215 132 NA 2215 NA NA NA Mnod_86207748v20141116 hypothetical protein 1208 133 1208 NA NA NA NA7749v20141116 integrase 134 134 NA NA 2875 NA NA 7751v20141116 integrasecatalytic 1210 136 1210 NA NA NA NA subunit 7782v20141116 hypotheticalprotein 2878 NA NA NA 2878 3597 NA 7783v20141116 GntR family 4116 NA NANA 2879 NA 4116 transcriptional regulator 7813v20141116 None 2883 NA NANA 2883 NA 4118 7814v20141116 hypothetical protein 2884 NA NA NA 2884 NA4119 7815v20141116 RNA polymerase 2885 NA NA NA 2885 NA 4120 subunitsigma-24 7829v20141116 hypothetical protein 1213 138 1213 NA NA NA NA7855v20141116 hypothetical protein 141 141 1216 NA NA NA NA7856v20141116 hypothetical protein 4125 142 NA NA NA NA 41257869v20141116 hypothetical protein 144 144 1218 NA NA NA NA Mchl_25887889v20141116 hypothetical protein 147 147 1222 NA NA NA NA Mnod_53477899v20141116 hypothetical protein 150 150 1224 NA NA NA NA7909v20141116 hypothetical protein 2217 152 NA 2217 NA NA NA Mpop_38367919v20141116 hypothetical protein 2895 NA 1230 NA 2895 NA NA7926v20141116 hypothetical protein 3604 NA NA NA NA 3604 41337931v20141116 None 3605 NA NA NA NA 3605 4134 7981v20141116 transposaseIS3/IS911 family protein 2909 NA NA NA 2909 NA 4141 8024v20141116short-chain 3609 NA NA 2220 NA 3609 NA dehydrogenase/reductase SDR8042v20141116 Hypothetical protein 156 156 1232 NA NA NA NA8052v20141116 MFS transporter 157 157 1233 NA NA NA NA 8092v20141116 ABCtransporter inner 4146 166 NA NA NA NA 4146 membrane protein8093v20141116 ABC transporter 167 167 NA NA NA NA 4147 8094v20141116nitrate/sulfonate/bicarbonate ABC 4148 168 NA NA NA NA 4148 transporter8098v20141116 hypothetical protein 170 170 1243 NA NA NA NA8113v20141116 adenylate/guanylate 4149 174 NA NA NA NA 4149 cyclase8115v20141116 integrase family 2910 176 NA NA 2910 NA NA protein8116v20141116 ISGsu7 transposase 177 177 1246 NA NA NA NA OrfA8117v20141116 hypothetical protein 178 178 1247 NA NA NA NAMrad2831_5711 8124v20141116 Mobile element 3611 NA 1249 NA NA 3611 NAprotein 8136v20141116 hypothetical protein 2230 NA NA 2230 2911 NA NAMpop_2878 8171v20141116 hypothetical protein 4155 NA NA NA 2912 NA 41558179v20141116 response regulator 2232 NA NA 2232 NA NA 4156 receiver8180v20141116 None 2233 NA NA 2233 NA NA 4157 8205v20141116 hypotheticalprotein 2917 NA NA NA 2917 NA 4160 8206v20141116 rhodanese 4161 NA NA NA2918 NA 4161 8237v20141116 integrase family 2919 NA NA NA 2919 3619 NAprotein 8258v20141116 hypothetical protein 180 180 NA NA NA 3620 NA8267v20141116 porin 181 181 1250 NA NA NA NA 8268v20141116 hypotheticalprotein 182 182 1251 NA NA NA NA Mrad2831_0222 8269v20141116hypothetical protein 183 183 1252 NA NA NA NA 8270v20141116 twocomponent 184 184 1253 NA NA NA NA transcriptional regulator8271v20141116 RND family efflux 185 185 1254 NA NA NA NA transporter MFPsubunit 8284v20141116 thiamine 187 187 1256 NA NA NA NA pyrophosphatebinding domain-containing protein 8299v20141116 hypothetical protein 190190 1258 NA NA NA NA 8301v20141116 None 4169 192 NA NA NA NA 41698308v20141116 hypothetical protein 194 194 1261 NA NA NA NA8311v20141116 enoyl-CoA hydratase 196 196 1263 NA NA NA NA 8332v20141116hypothetical protein 203 203 1269 NA NA NA NA BJ6T_24320 8334v20141116hypothetical protein 204 204 1270 NA NA NA NA 8339v20141116ATP-hydrolyzing 1272 NA 1272 2240 NA NA NA enzyme 8361v20141116 plasmidstability 3621 NA NA 2243 NA 3621 NA protein StbC 8411v20141116methyltransferase type 4180 NA NA NA NA 3627 4180 11 8412v20141116oxidoreductase 3628 NA NA NA NA 3628 4181 FAD/NAD(P)-bindingdomain-containing protein 8413v20141116 hypothetical protein 2929 NA NANA 2929 NA 4182 Mchl_5368 8445v20141116 integrase family 2937 NA NA NA2937 3629 NA protein 8450v20141116 hypothetical protein 4188 NA NA 2246NA NA 4188 GDI_3938 8463v20141116 linear gramicidin 1274 208 1274 NA NANA NA synthetase subunit C 8468v20141116 hypothetical protein 209 2091275 NA NA NA NA 8477v20141116 hypothetical protein 211 211 1277 NA NANA NA 8478v20141116 ABC transporter-like 212 212 1278 NA NA NA NAprotein 8479v20141116 acetamidase 213 213 1279 NA NA NA NA 8535v20141116C4-dicarboxylate ABC 216 216 1281 NA NA NA NA transporter 8536v20141116nitrate ABC transporter 217 217 1282 NA NA NA NA substrate-bindingprotein 8572v20141116 replication protein C 220 220 1285 NA NA NA NA8583v20141116 putative radical SAM 224 224 NA 2254 NA NA NA domainprotein 8588v20141116 4-carboxy 225 225 1288 NA NA NA NA muconolactonedecarboxylase 8598v20141116 LysR family 228 228 1291 NA NA NA NAtranscriptional regulator 8601v20141116 hypothetical protein 231 2311293 NA NA NA NA 8607v20141116 hypothetical protein 233 233 1295 NA NANA NA 8631v20141116 hypothetical protein 234 234 1296 NA NA NA NA8716v20141116 hypothetical protein 3638 NA NA NA NA 3638 41968826v20141116 phage integrase 2960 NA NA 2262 2960 NA NA 8844v20141116transposase ISDvu2 239 239 1300 NA NA NA NA 8857v20141116 alpha/betahydrolase 241 241 1302 NA NA NA NA 8858v20141116 putative chemotaxis 242242 1303 NA NA NA NA phosphatase CheZ 8862v20141116 hypothetical protein243 243 1304 NA NA NA NA Swoo_4771 8870v20141116 methionine gamma- 246246 1306 NA NA NA NA lyase 8871v20141116 CoA-binding domain- 247 247 NANA 2970 NA NA containing protein 8892v20141116 metal dependent 248 2481307 NA NA NA NA phosphohydrolase 8894v20141116 hypothetical protein 249249 1308 NA NA NA NA 8900v20141116 mercuric reductase 252 252 1310 NA NANA NA 8903v20141116 MFS transporter 253 253 1311 NA NA NA NA8908v20141116 hypothetical protein 1314 256 1314 NA NA NA NAMrad2831_1442 8923v20141116 hypothetical protein 258 258 1316 NA NA NANA Mrad2831_5910 8924v20141116 Xaa-Pro 259 259 1317 NA NA NA NAaminopeptidase 8925v20141116 hypothetical protein 260 260 1318 NA NA NANA 8933v20141116 multi-sensor signal 267 267 1320 NA NA NA NAtransduction histidine kinase 8938v20141116 endoribonuclease L- 268 2681321 NA NA NA NA PSP 8940v20141116 hypothetical protein 269 269 1322 NANA NA NA 8941v20141116 hypothetical protein 1323 270 1323 NA NA NA NA8947v20141116 hypothetical protein 1324 271 1324 NA NA NA NA8949v20141116 hypothetical protein 272 272 1325 NA NA NA NA Mnod_59358963v20141116 ATPase AAA 4207 NA 1328 NA NA NA 4207 8968v20141116 None4208 NA 1330 NA NA NA 4208 8975v20141116 two component LuxR 1333 NA 1333NA NA NA 4209 family transcriptional regulator 9009v20141116 LysR family2270 NA NA 2270 NA 3651 NA transcriptional regulator 9033v20141116cobyrinic acid ac- 2975 NA NA NA 2975 NA 4211 diamide synthase9049v20141116 hypothetical protein 2272 NA NA 2272 2977 NA NAMrad2831_5209 9054v20141116 hypothetical protein 3656 NA NA NA NA 36564213 MexAM1_META1p1280 9082v20141116 None 2273 NA NA 2273 NA NA 42149083v20141116 hypothetical protein 2274 NA NA 2274 NA NA 42159087v20141116 short-chain 4216 NA NA 2275 NA NA 4216 dehydrogenase9112v20141116 hypothetical protein 4221 NA NA NA NA 3659 42219113v20141116 hypothetical protein 3660 NA NA NA NA 3660 42229114v20141116 tricarboxylate 4223 NA NA NA NA 3661 4223 transporter9117v20141116 hypothetical protein 2981 NA NA NA 2981 NA 4225 Mchl_53719125v20141116 hypothetical protein 2986 NA NA NA 2986 3662 NA Mchl_07159136v20141116 hypothetical protein 3663 NA NA NA NA 3663 4235 Mnod_63469205v20141116 hypothetical protein 276 276 1334 NA NA NA NA9230v20141116 acetyl-CoA 278 278 1336 NA NA NA NA acetyltransferase9241v20141116 hypothetical protein 279 279 1338 NA NA NA NA9245v20141116 family 1 extracellular 281 281 1339 NA NA NA NAsolute-binding protein 9247v20141116 two-component sensor 282 282 1340NA NA NA NA histidine kinase 9254v20141116 carboxymethylenebutenolidase283 283 1342 NA NA NA NA 9257v20141116 hypothetical protein 284 284 1343NA NA NA NA 9260v20141116 beta-lactamase 285 285 1344 NA NA NA NAdomain-containing protein 9261v20141116 nucleotide sugar 286 286 1345 NANA NA NA dehydrogenase 9268v20141116 carbon monoxide 287 287 1346 NA NANA NA dehydrogenase 9269v20141116 hypothetical protein 288 288 1347 NANA NA NA 9270v20141116 peptidase M19 289 289 1348 NA NA NA NA9271v20141116 hypothetical protein 1349 290 1349 NA NA NA NA9278v20141116 hypothetical protein 294 294 1353 NA NA NA NA9281v20141116 glycosyl transferase 296 296 1355 NA NA NA NA family 19282v20141116 substrate-binding 297 297 NA 2280 NA NA NA protein9283v20141116 integral membrane 1356 298 1356 NA NA NA NA sensor hybridhistidine kinase 9284v20141116 acyltransferase 3 299 299 1357 NA NA NANA 9290v20141116 diguanylate cyclase 300 300 NA NA NA NA 42459291v20141116 hypothetical protein 301 301 NA 2281 NA NA NA9292v20141116 hypothetical protein 302 302 NA 2282 NA NA NA9295v20141116 hypothetical protein 303 303 1358 NA NA NA NA9297v20141116 hypothetical protein 1359 304 1359 NA NA NA NA9298v20141116 hypothetical protein 306 306 1360 NA NA NA NAMrad2831_0240 9300v20141116 nitrate ABC transporter 307 307 1361 NA NANA NA ATP-binding protein 9309v20141116 XRE family 4246 310 NA NA NA NA4246 transcriptional regulator 9311v20141116 Hypothetical protein 311311 1362 NA NA NA NA 9313v20141116 hypothetical protein 1363 312 1363 NANA NA NA 9315v20141116 hypothetical protein 313 313 1364 NA NA NA NA9321v20141116 nucleotidyltransferase 315 315 1366 NA NA NA NA9331v20141116 PadR family 317 317 1368 NA NA NA NA transcriptionalregulator 9347v20141116 ABC transporter inner 2994 NA 1373 NA 2994 NA NAmembrane protein 9348v20141116 hypothetical protein 4247 NA 1374 NA NANA 4247 9467v20141116 hypothetical protein 2287 NA NA 2287 NA NA 42539504v20141116 hypothetical protein 3674 NA NA NA 3007 3674 NA Mnod_48829669v20141116 Hypothetical protein 1376 319 1376 NA NA NA NA9675v20141116 conserved hypothetical 3017 NA NA NA 3017 3676 NA protein9680v20141116 NUDIX hydrolase 322 322 1377 NA NA NA NA 9687v20141116polysaccharide 323 323 1378 NA NA NA NA biosynthesis protein9689v20141116 fumarylacetoacetate 324 324 1380 NA NA NA NA (FAA)hydrolase 9690v20141116 hypothetical protein 325 325 1381 NA NA NA NAMrad2831_3421 9692v20141116 muconolactone delta- 327 327 1382 NA NA NANA isomerase 9693v20141116 shkimate 328 328 1383 NA NA NA NAdehydrogenase 9694v20141116 alcohol dehydrogenase 329 329 1384 NA NA NANA 9695v20141116 TadE family protein 330 330 1385 NA NA NA NA9696v20141116 hypothetical protein 331 331 1386 NA NA NA NA9698v20141116 hypothetical protein 332 332 1388 NA NA NA NA9701v20141116 membrane protein 333 333 1389 NA NA NA NA 9702v20141116MFS transporter 334 334 1390 NA NA NA NA 9703v20141116 Transcriptional335 335 1391 NA NA NA NA regulator GntR family 9707v20141116hypothetical protein 336 336 1392 NA NA NA NA 9708v20141116 phosphateABC 337 337 1393 NA NA NA NA transporter substrate- binding protein9709v20141116 ferredoxin 338 338 1394 NA NA NA NA 9710v20141116hypothetical protein 339 339 1395 NA NA NA NA Mrad2831_02209712v20141116 hypothetical protein 340 340 1396 NA NA NA NA9717v20141116 GntR family 1397 342 1397 NA NA NA NA transcriptionalregulator 9718v20141116 hypothetical protein 1398 343 1398 NA NA NA NA9719v20141116 monooxygenase FAD- 344 344 1400 NA NA NA NA bindingprotein 9720v20141116 hypothetical protein 345 345 1401 NA NA NA NAMrad2831_1283 9725v20141116 hypothetical protein 1402 347 1402 NA NA NANA 9727v20141116 hypothetical protein 348 348 1403 NA NA NA NA9728v20141116 hypothetical protein 349 349 1404 NA NA NA NA9730v20141116 hypothetical protein 350 350 1405 NA NA NA NA9731v20141116 amidase 351 351 1406 NA NA NA NA 9732v20141116hypothetical protein 352 352 1407 NA NA NA NA 9735v20141116 hypotheticalprotein 353 353 1408 NA NA NA NA 9736v20141116 methyl-accepting 1409 NA1409 NA NA NA 4279 chemotaxis protein 9739v20141116 hypothetical protein354 354 1410 NA NA NA NA 9744v20141116 hypothetical protein 355 355 1411NA NA NA NA 9745v20141116 alpha/beta hydrolase 356 356 1413 NA NA NA NAfold protein 9749v20141116 hypothetical protein 357 357 1414 NA NA NA NAMrad2831_1349 9750v20141116 carbon monoxide 358 358 1415 NA NA NA NAdehydrogenase 9751v20141116 hypothetical protein 1416 359 1416 NA NA NANA 9752v20141116 glyoxalase 360 360 1417 NA NA NA NA 9754v20141116hypothetical protein 1418 361 1418 NA NA NA NA 9759v20141116hypothetical protein 366 366 NA 2291 NA NA NA 9761v20141116 UDP-glucose6- 367 367 1420 NA NA NA NA dehydrogenase 9763v20141116 Hypotheticalprotein 369 369 1421 NA NA NA NA 9766v20141116 LysR family 370 370 1422NA NA NA NA transcriptional regulator 9769v20141116 glutathione S- 371371 1423 NA NA NA NA transferase 9776v20141116 hypothetical protein 4282NA NA NA 3019 NA 4282 Msil_2170 9778v20141116 peptidase S8 1425 375 1425NA NA NA NA 9787v20141116 LuxR family 377 377 1427 NA NA NA NAtranscriptional regulator 9789v20141116 hypothetical protein 378 3781428 NA NA NA NA 9790v20141116 hypothetical protein 379 379 1429 NA NANA NA 9791v20141116 hypothetical protein 380 380 1430 NA NA NA NA9796v20141116 cyclic nucleotide- 1431 382 1431 NA NA NA NA bindingprotein 9802v20141116 hypothetical protein 3679 NA 1432 NA NA 3679 NAMrad2831_5170 9804v20141116 Holliday junction ATP- 4283 NA 1433 NA NA NA4283 dependent DNA helicase 9989v20141116 Hypothetical protein 2297 NANA 2297 NA NA 4288 10005v20141116 Hypothetical protein 4289 NA NA NA NA3684 4289 10053v20141116 hypothetical protein 3033 NA NA NA 3033 3690 NAMchl_4474 10058v20141116 hypothetical protein 3039 NA NA NA 3039 NA 4296Mnod_7738 10065v20141116 NAD-dependent malic 4302 NA NA NA NA 3691 4302enzyme mitochondrial 10194v20141116 RTX toxins and related 385 385 NA NANA NA 4331 Ca2+-binding protein 10195v20141116 hypothetical protein 386386 1440 NA NA NA NA 10216v20141116 hypothetical protein 388 388 1442 NANA NA NA 10219v20141116 hypothetical protein 390 390 1443 NA NA NA NA10247v20141116 hypothetical protein 395 395 1450 NA NA NA NA10250v20141116 hypothetical protein 1451 397 1451 NA NA NA NA10251v20141116 hypothetical protein 398 398 1452 NA NA NA NA10252v20141116 hypothetical protein 399 399 1453 NA NA NA NA10253v20141116 histidine kinase 400 400 1454 NA NA NA NA 10254v20141116hypothetical protein 401 401 1455 NA NA NA NA Mnod_1661 10255v20141116peroxidase 402 402 1456 NA NA NA NA 10256v20141116 sn-glycerol-3- 1457403 1457 NA NA NA NA phosphate transporter 10257v20141116 hypotheticalprotein 1458 404 1458 NA NA NA NA 10258v20141116 acyl-CoA 405 405 1459NA NA NA NA dehydrogenase 10259v20141116 IclR family 406 406 1460 NA NANA NA transcriptional regulator 10260v20141116 aldehyde 407 407 1461 NANA NA NA dehydrogenase 10261v20141116 Dihydrodipicolinate 408 408 1462NA NA NA NA synthase 10264v20141116 hypothetical protein 410 410 1464 NANA NA NA 10265v20141116 None 411 411 1465 NA NA NA NA 10266v20141116hypothetical protein 412 412 1466 NA NA NA NA 10268v20141116hypothetical protein 413 413 1467 NA NA NA NA Atu3845 10269v20141116hypothetical protein 414 414 1468 NA NA NA NA 10272v20141116hypothetical protein 1469 415 1469 NA NA NA NA 10277v20141116 TetRfamily 417 417 1470 NA NA NA NA transcriptional regulator 10278v20141116hypothetical protein 418 418 1471 NA NA NA NA 10280v20141116hypothetical protein 1473 420 1473 NA NA NA NA MexAM1_META2p114610282v20141116 hypothetical protein 421 421 1474 NA NA NA NAMrad2831_4849 10283v20141116 citrate synthase 422 422 1475 NA NA NA NA10284v20141116 oxidoreductase 423 423 1476 NA NA NA NA 10285v20141116hypothetical protein 424 424 1477 NA NA NA NA 10286v20141116hypothetical protein 1478 425 1478 NA NA NA NA 10287v20141116 majorfacilitator 426 426 1479 NA NA NA NA superfamily protein 10290v20141116hypothetical protein 1480 427 1480 NA NA NA NA 10291v20141116 MFStransporter 428 428 1481 NA NA NA NA 10292v20141116 aldehyde 429 4291482 NA NA NA NA dehydrogenase 10293v20141116 GntR family 430 430 1483NA NA NA NA transcriptional regulator 10294v20141116 thioesterase 431431 1484 NA NA NA NA 10295v20141116 hypothetical protein 432 432 1485 NANA NA NA 10296v20141116 hypothetical protein 433 433 1486 NA NA NA NA10298v20141116 hypothetical protein 1487 434 1487 NA NA NA NA10299v20141116 hypothetical protein 435 435 1488 NA NA NA NA10300v20141116 MFS transporter 436 436 1489 NA NA NA NA 10301v20141116crotonase 437 437 1490 NA NA NA NA 10302v20141116 AMP-dependent 438 4381491 NA NA NA NA synthetase and ligase 10303v20141116 (2Fe—2S)-binding439 439 1492 NA NA NA NA domain-containing protein 10304v20141116transcriptional 440 440 1493 NA NA NA NA regulator 10305v20141116hydrolase 441 441 1494 NA NA NA NA 10306v20141116 twin-arginine 1495 4421495 NA NA NA NA translocation pathway signal 10307v20141116hypothetical protein 443 443 1496 NA NA NA NA 10309v20141116hypothetical protein 444 444 1497 NA NA NA NA 10310v20141116hypothetical protein 445 445 1498 NA NA NA NA 10313v20141116hypothetical protein 446 446 1499 NA NA NA NA 10315v20141116hypothetical protein 1500 447 1500 NA NA NA NA 10316v20141116 group 1glycosyl 448 448 1501 NA NA NA NA transferase 10317v20141116 group 1glycosyl 449 449 1502 NA NA NA NA transferase 10318v20141116non-specific protein- 450 450 1503 NA NA NA NA tyrosine kinase10319v20141116 hypothetical protein 1504 451 1504 NA NA NA NA10323v20141116 AraC family 452 452 NA 2306 NA NA NA transcriptionalregulator 10324v20141116 hypothetical protein 2307 453 NA 2307 NA NA NA10326v20141116 aminotransferase class 2308 454 NA 2308 NA NA NA I/II10328v20141116 hypothetical protein 455 455 1506 NA NA NA NA10331v20141116 acyl-CoA 458 458 1508 NA NA NA NA dehydrogenase10334v20141116 hypothetical protein 459 459 1509 NA NA NA NA10335v20141116 hypothetical protein 460 460 NA NA NA NA 4342 Mnod_773310337v20141116 hypothetical protein 1510 462 1510 NA NA NA NA10341v20141116 glyoxalase/bleomycin 463 463 1511 NA NA NA NA resistanceprotein/dioxygenase 10343v20141116 CitMHS family 1512 464 1512 NA NA NANA citrate/H+ symporter 10344v20141116 ABC transporter 465 465 1513 NANA NA NA substrate-binding protein 10345v20141116 beta-lactamase 466 4661514 NA NA NA NA 10346v20141116 endoribonuclease L- 1515 467 1515 NA NANA NA PSP 10347v20141116 hypothetical protein 1516 468 1516 NA NA NA NAMrad2831_4429 10349v20141116 hypothetical protein 1518 470 1518 NA NA NANA 10350v20141116 hypothetical protein 1519 471 1519 NA NA NA NA10354v20141116 Hypothetical protein 4343 472 NA NA NA NA 434310356v20141116 Hypothetical protein 473 473 1520 NA NA NA NA10358v20141116 hypothetical protein 474 474 NA NA NA NA 434510361v20141116 hypothetical protein 1522 NA 1522 NA NA NA 4346Mrad2831_5665 10655v20141116 hypothetical protein 2312 NA NA 2312 3049NA NA 10656v20141116 hypothetical protein 2313 NA NA 2313 3050 NA NAMrad2831_5208 10675v20141116 transposase 3697 NA NA 2314 NA 3697 NA10688v20141116 None 2316 NA NA 2316 NA NA 4354 10941v20141116hypothetical protein 1529 475 1529 NA NA NA NA 10942v20141116peptidoglycan-binding 478 478 1530 NA NA NA NA protein 10980v20141116hypothetical protein 1534 479 1534 NA NA NA NA 10994v20141116hypothetical protein 1535 480 1535 NA NA NA NA 10999v20141116hypothetical protein 482 482 1536 NA NA NA NA 11000v20141116hypothetical protein 483 483 1537 NA NA NA NA 11001v20141116 ABCtransporter 484 484 1538 NA NA NA NA permease 11002v20141116hypothetical protein 485 485 1539 NA NA NA NA 11003v201411163-ketoacyl-ACP 486 486 1540 NA NA NA NA reductase 11004v20141116branched-chain amino 487 487 1541 NA NA NA NA acid ABC transporterATP-binding protein 11005v20141116 NADPH quinone 488 488 1542 NA NA NANA oxidoreductase 11006v20141116 hypothetical protein 489 489 1543 NA NANA NA 11007v20141116 hypothetical protein 490 490 1544 NA NA NA NA11008v20141116 aliphatic amidase 491 491 1545 NA NA NA NAexpression-regulating protein AmiC 11009v20141116 hypothetical protein492 492 1546 NA NA NA NA 11010v20141116 short-chain 493 493 1547 NA NANA NA dehydrogenase/reductase SDR 11013v20141116 hypothetical protein494 494 1548 NA NA NA NA 11014v20141116 hypothetical protein 495 4951549 NA NA NA NA 11015v20141116 hypothetical protein 496 496 1550 NA NANA NA 11016v20141116 ECF subfamily RNA 497 497 1551 NA NA NA NApolymerase sigma-24 factor 11019v20141116 major facilitator 498 498 1552NA NA NA NA transporter 11022v20141116 hypothetical protein 499 499 1553NA NA NA NA Mrad2831_2880 11023v20141116 hypothetical protein 1554 5001554 NA NA NA NA 11024v20141116 hypothetical protein 501 501 1555 NA NANA NA 11025v20141116 hypothetical protein 502 502 1556 NA NA NA NA11026v20141116 None 503 503 1557 NA NA NA NA 11027v20141116 helicase 504504 1558 NA NA NA NA 11029v20141116 Hypothetical protein 1559 506 1559NA NA NA NA 11030v20141116 hypothetical protein 1560 507 1560 NA NA NANA 11031v20141116 hypothetical protein 508 508 1561 NA NA NA NAMrad2831_3995 11032v20141116 hypothetical protein 509 509 1562 NA NA NANA 11033v20141116 hypothetical protein 510 510 1563 NA NA NA NA11034v20141116 hypothetical protein 511 511 1564 NA NA NA NA11035v20141116 fatty acid hydroxylase 512 512 1565 NA NA NA NA11036v20141116 DNA-binding two- 513 513 1566 NA NA NA NA componentresponse regulator 11037v20141116 hypothetical protein 514 514 1567 NANA NA NA 11038v20141116 hypothetical protein 515 515 1568 NA NA NA NA11040v20141116 hypothetical protein 516 516 1569 NA NA NA NAMrad2831_4848 11041v20141116 hypothetical protein 517 517 1570 NA NA NANA Mrad2831_4850 11042v20141116 AraC family 518 518 1571 NA NA NA NAtranscriptional regulator 11043v20141116 MucR family 1572 519 1572 NA NANA NA transcriptional regulator 11044v20141116 hypothetical protein 520520 1573 NA NA NA NA 11045v20141116 hypothetical protein 521 521 1574 NANA NA NA 11046v20141116 hypothetical protein 522 522 1575 NA NA NA NA11047v20141116 hypothetical protein 523 523 1576 NA NA NA NAMrad2831_4872 11048v20141116 MucR family 524 524 1577 NA NA NA NAtranscriptional regulator 11049v20141116 hypothetical protein 525 5251578 NA NA NA NA 11050v20141116 hypothetical protein 526 526 1579 NA NANA NA 11051v20141116 hypothetical protein 1580 527 1580 NA NA NA NA11053v20141116 hypothetical protein 528 528 1581 NA NA NA NA11055v20141116 hypothetical protein 529 529 1582 NA NA NA NA11056v20141116 hypothetical protein 530 530 1583 NA NA NA NA11058v20141116 CDP-diacylglycerol 531 531 1584 NA NA NA NA diphosphatase11059v20141116 hypothetical protein 532 532 1585 NA NA NA NA11060v20141116 hypothetical protein 533 533 1586 NA NA NA NA11062v20141116 hypothetical protein 534 534 1587 NA NA NA NA11065v20141116 hypothetical protein 1588 535 1588 NA NA NA NAMrad2831_4173 11066v20141116 hypothetical protein 536 536 1589 NA NA NANA 11067v20141116 hypothetical protein 1590 537 1590 NA NA NA NA11068v20141116 hypothetical protein 538 538 1591 NA NA NA NA11069v20141116 hypothetical protein 539 539 1592 NA NA NA NA11071v20141116 hypothetical protein 540 540 1593 NA NA NA NA11072v20141116 hypothetical protein 541 541 1594 NA NA NA NA11073v20141116 hypothetical protein 542 542 1595 NA NA NA NA11074v20141116 hypothetical protein 543 543 1596 NA NA NA NAMrad2831_2451 11075v20141116 hypothetical protein 1597 544 1597 NA NA NANA 11077v20141116 hypothetical protein 545 545 1598 NA NA NA NAMrad2831_4594 11078v20141116 hypothetical protein 546 546 1599 NA NA NANA Mrad2831_4604 11079v20141116 hypothetical protein 547 547 1600 NA NANA NA 11082v20141116 hypothetical protein 548 548 1601 NA NA NA NA11083v20141116 hypothetical protein 549 549 1602 NA NA NA NA11085v20141116 hypothetical protein 550 550 1603 NA NA NA NA11086v20141116 methyl-accepting 1604 551 1604 NA NA NA NA chemotaxissensory transducer 11087v20141116 hypothetical protein 1605 552 1605 NANA NA NA 11090v20141116 hypothetical protein 1606 553 1606 NA NA NA NA11091v20141116 hypothetical protein 554 554 1607 NA NA NA NA11092v20141116 putative 555 555 1608 NA NA NA NA transmembrane protein11093v20141116 hypothetical protein 556 556 1609 NA NA NA NAMrad2831_5620 11094v20141116 hypothetical protein 557 557 1610 NA NA NANA 11095v20141116 hypothetical protein 558 558 1611 NA NA NA NAMrad2831_5792 11096v20141116 hypothetical protein 559 559 1612 NA NA NANA 11097v20141116 hypothetical protein 560 560 1613 NA NA NA NA11098v20141116 hypothetical protein 561 561 1614 NA NA NA NA11099v20141116 hypothetical protein 562 562 1615 NA NA NA NA11100v20141116 hypothetical protein 563 563 1616 NA NA NA NA11101v20141116 hypothetical protein 564 564 1617 NA NA NA NA11102v20141116 hypothetical protein 565 565 1618 NA NA NA NA11103v20141116 HxlR family 566 566 1619 NA NA NA NA transcriptionalregulator 11105v20141116 hypothetical protein 567 567 1620 NA NA NA NAMrad2831_1263 11106v20141116 hypothetical protein 568 568 1621 NA NA NANA Mrad2831_1264 11108v20141116 hypothetical protein 569 569 1622 NA NANA NA 11109v20141116 type III effector Hrp- 570 570 1623 NA NA NA NAdependent protein 11110v20141116 hypothetical protein 1624 571 1624 NANA NA NA 11114v20141116 hypothetical protein 573 573 1625 NA NA NA NA11117v20141116 hypothetical protein 574 574 1626 NA NA NA NA11118v20141116 hypothetical protein 575 575 1627 NA NA NA NA11119v20141116 hypothetical protein 1628 576 1628 NA NA NA NA11121v20141116 hypothetical protein 578 578 1630 NA NA NA NA11125v20141116 hypothetical protein 581 581 1631 NA NA NA NA11126v20141116 hypothetical protein 582 582 1632 NA NA NA NAMrad2831_4291 11127v20141116 hypothetical protein 583 583 1633 NA NA NANA 11128v20141116 putative aldo/keto 1634 584 1634 NA NA NA NA reductaseprotein 11129v20141116 hypothetical protein 585 585 1635 NA NA NA NAMrad2831_1223 11130v20141116 hypothetical protein 586 586 1636 NA NA NANA 11131v20141116 hypothetical protein 587 587 1637 NA NA NA NA11134v20141116 hypothetical protein 589 589 1638 NA NA NA NA11136v20141116 hypothetical protein 590 590 1639 NA NA NA NAMrad2831_4454 11137v20141116 phosphoglycolate 1640 591 1640 NA NA NA NAphosphatase 11138v20141116 substrate-binding 592 592 1641 NA NA NA NAprotein 11139v20141116 hypothetical protein 1642 593 1642 NA NA NA NA11140v20141116 FAD-dependent 1643 594 1643 NA NA NA NA pyridinenucleotide- disulfide oxidoreductase 11141v20141116 hypothetical protein1644 595 1644 NA NA NA NA 11142v20141116 5-oxopent-3-ene-1 2 5- 596 5961645 NA NA NA NA tricarboxylate decarboxylase 11143v20141116hypothetical protein 1646 597 1646 NA NA NA NA Mrad2831_190411149v20141116 hypothetical protein 600 600 1647 NA NA NA NA11150v20141116 hypothetical protein 601 601 1648 NA NA NA NAMrad2831_1911 11151v20141116 hypothetical protein 602 602 1649 NA NA NANA 11152v20141116 hypothetical protein 603 603 1650 NA NA NA NA11153v20141116 hypothetical protein 604 604 1651 NA NA NA NA11154v20141116 hypothetical protein 605 605 1652 NA NA NA NA11155v20141116 hypothetical protein 606 606 1653 NA NA NA NA11156v20141116 methyl-accepting 1654 607 1654 NA NA NA NA chemotaxissensory transducer 11157v20141116 hypothetical protein 608 608 1655 NANA NA NA 11161v20141116 MucR family 610 610 1656 NA NA NA NAtranscriptional regulator 11162v20141116 hypothetical protein 611 6111657 NA NA NA NA 11164v20141116 hypothetical protein 612 612 1658 NA NANA NA 11165v20141116 MarR family 613 613 1659 NA NA NA NAtranscriptional regulator 11167v20141116 capsule polysaccharide 614 6141660 NA NA NA NA transporter 11168v20141116 hypothetical protein 615 6151661 NA NA NA NA 11169v20141116 hypothetical protein 616 616 1662 NA NANA NA 11171v20141116 hypothetical protein 617 617 1663 NA NA NA NA11172v20141116 hypothetical protein 618 618 1664 NA NA NA NAMrad2831_1654 11176v20141116 hypothetical protein 619 619 1665 NA NA NANA 11177v20141116 hypothetical protein 620 620 1666 NA NA NA NA11178v20141116 hypothetical protein 621 621 1667 NA NA NA NA11180v20141116 hypothetical protein 624 624 1668 NA NA NA NA11181v20141116 hypothetical protein 625 625 1669 NA NA NA NA11182v20141116 hypothetical protein 626 626 1670 NA NA NA NA11183v20141116 hypothetical protein 627 627 1671 NA NA NA NA11184v20141116 hypothetical protein 1672 628 1672 NA NA NA NA11185v20141116 hypothetical protein 1673 629 1673 NA NA NA NA11186v20141116 hypothetical protein 630 630 1674 NA NA NA NA11187v20141116 hypothetical protein 631 631 1675 NA NA NA NA11188v20141116 GntR family 1676 633 1676 NA NA NA NA transcriptionalregulator 11189v20141116 hypothetical protein 634 634 1677 NA NA NA NAMrad2831_2999 11190v20141116 hypothetical protein 635 635 1678 NA NA NANA 11191v20141116 Hypothetical protein 1679 636 1679 NA NA NA NA11193v20141116 haloacid dehalogenase 637 637 1680 NA NA NA NA11196v20141116 hypothetical protein 1681 638 1681 NA NA NA NA11197v20141116 Holliday junction DNA 639 639 1682 NA NA NA NA helicaseRuvB 11198v20141116 hypothetical protein 640 640 1683 NA NA NA NApartial 11199v20141116 hypothetical protein 641 641 1684 NA NA NA NA11200v20141116 hypothetical protein 642 642 1685 NA NA NA NA11201v20141116 hypothetical protein 643 643 1686 NA NA NA NA11203v20141116 hypothetical protein 1687 644 1687 NA NA NA NAMrad2831_5411 11204v20141116 hypothetical protein 645 645 1688 NA NA NANA 11206v20141116 glycosyl transferase 1689 646 1689 NA NA NA NA familyprotein 11207v20141116 hypothetical protein 1690 647 1690 NA NA NA NA11213v20141116 hypothetical protein 3075 NA 1692 NA 3075 NA NA Mchl_164511233v20141116 None 1706 NA 1706 NA NA NA 4407 11447v20141116 None 3088NA NA NA 3088 3711 NA 11497v20141116 None 2323 NA NA 2323 NA NA 442011506v20141116 amidase 2324 NA NA 2324 NA NA 4422 11507v20141116 ABCtransporter ATP- 4423 NA NA 2325 NA NA 4423 binding protein11508v20141116 nitrate/sulfonate/bicarbonate 4424 NA NA 2326 NA NA 4424ABC transporter periplasmic protein 11511v20141116 None 4425 NA NA 2327NA NA 4425 11576v20141116 hypothetical protein 3103 NA NA NA 3103 NA4436 12016v20141116 hypothetical protein 1708 651 1708 NA NA NA NA12018v20141116 hypothetical protein 653 653 1709 NA NA NA NA12020v20141116 hypothetical protein 654 654 1710 NA NA NA NA12021v20141116 transcriptional 655 655 1711 NA NA NA NA regulator12022v20141116 hypothetical protein 656 656 1712 NA NA NA NAMrad2831_0355 12025v20141116 hypothetical protein 658 658 1713 NA NA NANA 12026v20141116 hypothetical protein 659 659 1714 NA NA NA NA12027v20141116 hypothetical protein 660 660 1715 NA NA NA NA12028v20141116 hypothetical protein 661 661 1716 NA NA NA NA12029v20141116 hypothetical protein 662 662 1717 NA NA NA NA12030v20141116 hypothetical protein 663 663 1718 NA NA NA NA12031v20141116 hypothetical protein 664 664 1719 NA NA NA NA12032v20141116 hypothetical protein 665 665 1720 NA NA NA NA12033v20141116 hypothetical protein 666 666 1721 NA NA NA NA12034v20141116 MFS transporter 667 667 1722 NA NA NA NA 12035v201411163-hydroxyisobutyrate 668 668 1723 NA NA NA NA dehydrogenase12036v20141116 gamma- 669 669 1724 NA NA NA NA carboxymuconolactonedecarboxylase 12037v20141116 None 670 670 1725 NA NA NA NA12039v20141116 hypothetical protein 671 671 1726 NA NA NA NA12040v20141116 hypothetical protein 1727 672 1727 NA NA NA NA12041v20141116 None 673 673 1728 NA NA NA NA 12043v20141116 None 674 6741729 NA NA NA NA 12044v20141116 None 675 675 1730 NA NA NA NA12045v20141116 None 676 676 1731 NA NA NA NA 12046v20141116 None 677 6771732 NA NA NA NA 12047v20141116 None 678 678 1733 NA NA NA NA12048v20141116 None 679 679 1734 NA NA NA NA 12049v20141116 hypotheticalprotein 680 680 1735 NA NA NA NA 12050v20141116 hypothetical protein 681681 1736 NA NA NA NA 12051v20141116 None 682 682 1737 NA NA NA NA12052v20141116 None 683 683 1738 NA NA NA NA 12053v20141116 hypotheticalprotein 684 684 1739 NA NA NA NA 12054v20141116 None 685 685 1740 NA NANA NA 12055v20141116 hypothetical protein 1741 686 1741 NA NA NA NA12056v20141116 hypothetical protein 687 687 1742 NA NA NA NA12057v20141116 acetyltransferase 688 688 1743 NA NA NA NA GNAT family12058v20141116 hypothetical protein 689 689 1744 NA NA NA NA Msil_310812059v20141116 hypothetical protein 690 690 1745 NA NA NA NA12060v20141116 hypothetical protein 691 691 1746 NA NA NA NA12061v20141116 None 692 692 1747 NA NA NA NA 12062v20141116 hypotheticalprotein 693 693 1748 NA NA NA NA 12063v20141116 hypothetical protein 694694 1749 NA NA NA NA 12064v20141116 hypothetical protein 695 695 1750 NANA NA NA 12065v20141116 None 696 696 1751 NA NA NA NA 12066v20141116hypothetical protein 697 697 1752 NA NA NA NA 12067v20141116hypothetical protein 698 698 1753 NA NA NA NA AZOLI_2591 12068v20141116None 699 699 1754 NA NA NA NA 12071v20141116 None 702 702 NA NA NA NA4635 12073v20141116 hypothetical protein 703 703 1755 NA NA NA NA12074v20141116 hypothetical protein 704 704 1756 NA NA NA NA12076v20141116 hypothetical protein 1757 705 1757 NA NA NA NA12077v20141116 cystathionine beta- 706 706 1758 NA NA NA NA lyase12078v20141116 hypothetical protein 707 707 1759 NA NA NA NA12079v20141116 hypothetical protein 708 708 1760 NA NA NA NA12080v20141116 None 709 709 1761 NA NA NA NA 12081v20141116prevent-host-death 710 710 1762 NA NA NA NA protein 12082v20141116hypothetical protein 711 711 1763 NA NA NA NA 12083v20141116 ABCtransporter 712 712 1764 NA NA NA NA permease 12085v20141116 None 713713 1765 NA NA NA NA 12086v20141116 hypothetical protein 1766 714 1766NA NA NA NA 12087v20141116 hypothetical protein 715 715 1767 NA NA NA NA12089v20141116 histone 716 716 1768 NA NA NA NA acetyltransferase12091v20141116 TetR family 717 717 1769 NA NA NA NA transcriptionalregulator 12092v20141116 None 718 718 1770 NA NA NA NA 12093v20141116hypothetical protein 1771 719 1771 NA NA NA NA 12095v20141116hypothetical protein 720 720 1772 NA NA NA NA 12097v20141116hypothetical protein 722 722 1773 NA NA NA NA 12099v20141116hypothetical protein 723 723 1774 NA NA NA NA Mrad2831_456112100v20141116 hypothetical protein 724 724 1775 NA NA NA NA12103v20141116 endo-1 3-beta- 725 725 1776 NA NA NA NA glucanase12104v20141116 hypothetical protein 726 726 1777 NA NA NA NA12105v20141116 hypothetical protein 727 727 1778 NA NA NA NA12106v20141116 hypothetical protein 728 728 1779 NA NA NA NA12107v20141116 hypothetical protein 729 729 1780 NA NA NA NA12108v20141116 hypothetical protein 730 730 1781 NA NA NA NA12110v20141116 hypothetical protein 1782 731 1782 NA NA NA NA12111v20141116 hypothetical protein 732 732 1783 NA NA NA NA12112v20141116 hypothetical protein 733 733 1784 NA NA NA NA12113v20141116 hypothetical protein 734 734 1785 NA NA NA NA12115v20141116 hypothetical protein 735 735 1786 NA NA NA NA12116v20141116 hypothetical protein 736 736 1787 NA NA NA NA12117v20141116 hypothetical protein 737 737 1788 NA NA NA NAMrad2831_2464 12118v20141116 hypothetical protein 738 738 1789 NA NA NANA 12119v20141116 hypothetical protein 739 739 1790 NA NA NA NAMrad2831_4587 12121v20141116 hypothetical protein 740 740 1791 NA NA NANA Mrad2831_4596 12122v20141116 aldehyde 741 741 1792 NA NA NA NAdehydrogenase 12123v20141116 hypothetical protein 742 742 1793 NA NA NANA 12124v20141116 hypothetical protein 743 743 1794 NA NA NA NA12125v20141116 transcriptional 744 744 1795 NA NA NA NA regulator12126v20141116 hypothetical protein 745 745 1796 NA NA NA NA12127v20141116 hypothetical protein 746 746 1797 NA NA NA NA12129v20141116 hypothetical protein 747 747 1798 NA NA NA NA12130v20141116 coenzyme PQQ 748 748 1799 NA NA NA NA biosynthesisprotein A 12132v20141116 hypothetical protein 749 749 1800 NA NA NA NA12133v20141116 None 750 750 1801 NA NA NA NA 12134v20141116 hypotheticalprotein 751 751 1802 NA NA NA NA 12135v20141116 hypothetical protein 752752 1803 NA NA NA NA 12136v20141116 hypothetical protein 753 753 1804 NANA NA NA 12137v20141116 hypothetical protein 754 754 1805 NA NA NA NA12138v20141116 hypothetical protein 755 755 1806 NA NA NA NA12140v20141116 hypothetical protein 1807 756 1807 NA NA NA NA12141v20141116 Hypothetical protein 757 757 1808 NA NA NA NA12142v20141116 hypothetical protein 758 758 1809 NA NA NA NA12143v20141116 hypothetical protein 759 759 1810 NA NA NA NA12144v20141116 hypothetical protein 760 760 1811 NA NA NA NA12145v20141116 hypothetical protein 761 761 1812 NA NA NA NA12146v20141116 deaminase reductase 762 762 1813 NA NA NA NA12147v20141116 hypothetical protein 763 763 1814 NA NA NA NA12149v20141116 hypothetical protein 765 765 1815 NA NA NA NA12151v20141116 histidine kinase 767 767 1816 NA NA NA NA 12152v20141116hypothetical protein 768 768 1817 NA NA NA NA 12153v20141116hypothetical protein 769 769 1818 NA NA NA NA 12154v20141116hypothetical protein 770 770 1819 NA NA NA NA 12155v20141116hypothetical protein 771 771 1820 NA NA NA NA 12160v20141116hypothetical protein 772 772 1821 NA NA NA NA 12161v20141116hypothetical protein 4637 773 NA NA NA NA 4637 MexAM1_META1p321412162v20141116 putative 774 774 1822 NA NA NA NA transmembrane protein12164v20141116 hypothetical protein 775 775 1823 NA NA NA NA12165v20141116 ABC transporter 776 776 NA 2328 NA NA NAsubstrate-binding protein family 5 12166v20141116 signal peptide protein1824 777 1824 NA NA NA NA 12167v20141116 hypothetical protein 778 7781825 NA NA NA NA 12168v20141116 hypothetical protein 779 779 1826 NA NANA NA 12169v20141116 hypothetical protein 780 780 1827 NA NA NA NA12170v20141116 hypothetical protein 781 781 1828 NA NA NA NA12171v20141116 hypothetical protein 782 782 1829 NA NA NA NA12172v20141116 hypothetical protein 783 783 1830 NA NA NA NA12173v20141116 hypothetical protein 784 784 1831 NA NA NA NA12174v20141116 adenylate cyclase 785 785 1832 NA NA NA NA 12175v20141116hypothetical protein 786 786 1833 NA NA NA NA 12176v20141116hypothetical protein 787 787 1834 NA NA NA NA 12177v20141116hypothetical protein 788 788 1835 NA NA NA NA Mrad2831_365712178v20141116 hypothetical protein 789 789 1836 NA NA NA NA12179v20141116 hypothetical protein 790 790 1837 NA NA NA NA12180v20141116 hypothetical protein 791 791 1838 NA NA NA NA12185v20141116 None 793 793 1839 NA NA NA NA 12186v20141116 hypotheticalprotein 1840 794 1840 NA NA NA NA 12187v20141116 hypothetical protein1841 795 1841 NA NA NA NA 12189v20141116 hypothetical protein 796 7961843 NA NA NA NA 12190v20141116 hypothetical protein 797 797 1844 NA NANA NA 12191v20141116 hypothetical protein 1845 798 1845 NA NA NA NA12192v20141116 oxidoreductase 799 799 1846 NA NA NA NA 12193v20141116hypothetical protein 800 800 1847 NA NA NA NA 12194v20141116hypothetical protein 801 801 1848 NA NA NA NA 12195v20141116hypothetical protein 1849 802 1849 NA NA NA NA 12196v20141116hypothetical protein 803 803 1850 NA NA NA NA 12197v20141116hypothetical protein 1851 804 1851 NA NA NA NA 12198v20141116 porin 1852805 1852 NA NA NA NA 12200v20141116 hypothetical protein 1853 806 1853NA NA NA NA 12202v20141116 hypothetical protein 807 807 1854 NA NA NA NAMrad2831_3327 12207v20141116 hypothetical protein 809 809 1855 NA NA NANA 12208v20141116 hypothetical protein 810 810 1856 NA NA NA NA12209v20141116 hypothetical protein 811 811 1857 NA NA NA NA12210v20141116 hypothetical protein 812 812 1858 NA NA NA NA12212v20141116 hypothetical protein 813 813 1859 NA NA NA NA12214v20141116 None 814 814 1860 NA NA NA NA 12217v20141116 hypotheticalprotein 816 816 1861 NA NA NA NA 12218v20141116 hypothetical protein 817817 1862 NA NA NA NA 12219v20141116 hypothetical protein 818 818 1863 NANA NA NA 12220v20141116 RNA polymerase sigma 819 819 1864 NA NA NA NAfactor SigJ 12221v20141116 hypothetical protein 820 820 1865 NA NA NA NA12222v20141116 hypothetical protein 1866 821 1866 NA NA NA NA12223v20141116 hypothetical protein 822 822 1867 NA NA NA NA12226v20141116 hypothetical protein 823 823 1868 NA NA NA NA12227v20141116 hypothetical protein 824 824 1869 NA NA NA NA12228v20141116 None 825 825 1870 NA NA NA NA 12230v20141116 hypotheticalprotein 1871 826 1871 NA NA NA NA 12231v20141116 hypothetical protein1872 827 1872 NA NA NA NA 12232v20141116 None 828 828 1873 NA NA NA NA12233v20141116 hypothetical protein 1874 829 1874 NA NA NA NA12234v20141116 PAS domain-containing 830 830 1875 NA NA NA NA protein12235v20141116 hypothetical protein 1876 831 1876 NA NA NA NA12236v20141116 hypothetical protein 832 832 1877 NA NA NA NA12237v20141116 None 833 833 1878 NA NA NA NA 12239v20141116 hypotheticalprotein 834 834 1879 NA NA NA NA 12240v20141116 None 835 835 1880 NA NANA NA 12241v20141116 hypothetical protein 836 836 1881 NA NA NA NA12242v20141116 hypothetical protein 837 837 1882 NA NA NA NA12244v20141116 AraC family 838 838 1883 NA NA NA NA transcriptionalregulator 12245v20141116 hypothetical protein 839 839 1884 NA NA NA NA12246v20141116 hypothetical protein 1885 840 1885 NA NA NA NA12248v20141116 hypothetical protein 1886 842 1886 NA NA NA NA12251v20141116 hypothetical protein 844 844 1887 NA NA NA NA12252v20141116 porin 845 845 1888 NA NA NA NA 12270v20141116hypothetical protein 4642 NA 1900 NA NA NA 4642 12282v20141116carbohydrate-selective 3725 NA 1905 NA NA 3725 NA porin OprB13420v20141116 hypothetical protein 3739 NA NA NA 3131 3739 NA Mchl_536314119v20141116 hypothetical protein 848 848 NA NA 3156 NA NA BBta_657314131v20141116 hypothetical protein 853 853 1912 NA NA NA NACcrKarma_gp008 14132v20141116 None 854 854 1913 NA NA NA NA14133v20141116 None 855 855 1914 NA NA NA NA 14134v20141116 None 856 8561915 NA NA NA NA 14136v20141116 None 857 857 1916 NA NA NA NA14137v20141116 None 858 858 1917 NA NA NA NA 14138v20141116 None 859 8591918 NA NA NA NA 14139v20141116 hypothetical protein 860 860 1919 NA NANA NA 14152v20141116 glycosyl transferase 867 867 1920 NA NA NA NAfamily protein 14156v20141116 None 869 869 1921 NA NA NA NA14168v20141116 integrase catalytic 1923 871 1923 NA NA NA NA region(modular protein) 14170v20141116 hypothetical protein 1925 872 1925 NANA NA NA 14172v20141116 Fis family 873 873 NA NA NA NA 4875transcriptional regulator 14174v20141116 hypothetical protein 874 8741926 NA NA NA NA Mrad2831_5180 14176v20141116 hypothetical protein 1927875 1927 NA NA NA NA 14181v20141116 magnesium chelatase 878 878 1929 NANA NA NA 14182v20141116 hypothetical protein 879 879 1930 NA NA NA NA14189v20141116 hypothetical protein 884 884 1931 NA NA NA NA14190v20141116 None 1932 885 1932 NA NA NA NA 14196v20141116 WGR domain-1934 889 1934 NA NA NA NA containing protein 14200v20141116 hypotheticalprotein 893 893 1935 NA NA NA NA 14291v20141116 hypothetical protein2020 NA 2020 2342 NA NA NA 14320v20141116 membrane protein 3160 NA 2046NA 3160 NA NA 14649v20141116 dienelactone hydrolase 3173 NA NA NA 31733768 NA 14657v20141116 hypothetical protein 3180 NA NA NA 3180 NA 488115376v20141116 transcriptional 2058 904 2058 NA NA NA NA regulator15391v20141116 hypothetical protein 916 916 2059 NA NA NA NA15392v20141116 None 917 917 2060 NA NA NA NA 15394v20141116 RluA family918 918 2061 NA NA NA NA pseudouridine synthase 15437v20141116 PASsensor protein 2063 938 2063 NA NA NA NA 15441v20141116 integrasecatalytic 940 940 2064 NA NA NA NA subunit 15442v20141116 hypotheticalprotein 2370 941 NA 2370 NA NA NA 15451v20141116 hypothetical protein946 946 2065 NA NA NA NA 15452v20141116 molecular chaperone 947 947 2066NA NA NA NA GroES 15460v20141116 epimerase 952 952 2067 NA NA NA NA15489v20141116 hypothetical protein 2371 NA 2085 2371 NA NA NA15815v20141116 hypothetical protein 3787 NA NA 2393 NA 3787 NA17689v20141116 None 993 993 2112 NA NA NA NA 17695v20141116 hypotheticalprotein 999 999 2113 NA NA NA NA 17705v20141116 None 1006 1006 2114 NANA NA NA 17706v20141116 hypothetical protein 2406 NA NA 2406 3251 NA NA17707v20141116 hypothetical protein 1007 1007 2115 NA NA NA NA17708v20141116 None 1008 1008 2116 NA NA NA NA 17709v20141116 None 10091009 2117 NA NA NA NA 17710v20141116 None 1010 1010 2118 NA NA NA NA17731v20141116 integrase catalytic 3252 1024 NA NA 3252 NA NA subunit17732v20141116 putative aspartate 2407 1025 NA 2407 NA NA NA racemase17757v20141116 None 2119 1041 2119 NA NA NA NA 17759v20141116hypothetical protein 2120 1042 2120 NA NA NA NA 17795v20141116hypothetical protein 1073 1073 2122 NA NA NA NA Mrad2831_425517807v20141116 glycosyl transferase 1085 1085 NA 2409 NA NA NA17808v20141116 hypothetical protein 2123 1086 2123 NA NA NA NA17857v20141116 polar amino acid ABC 2164 NA 2164 2410 NA NA NAtransporter permease 18264v20141116 hypothetical protein 3258 NA NA 24163258 NA NA Rleg2_4164

REFERENCES FOR EXAMPLE 8

-   1. Miller J R, Koren S, Sutton G (2010) Assembly algorithms for    next-generation sequencing data. Genomics 95: 315-327.-   2. Zerbino D R, Birney E (2008) Velvet: algorithms for de novo short    read assembly using de Bruijn graphs. Genome Res 18: 821-829.-   3. Delcher A L, Bratke K A, Powers E C, Salzberg S L (2007)    Identifying bacterial genes and endosymbiont DNA with Glimmer.    Bioinformatics 23: 673-679.-   4. Lowe T M, Eddy S R (1997) tRNAscan-SE: a program for improved    detection of transfer RNA genes in genomic sequence. Nucleic Acids    Res 25: 955-964.-   5. Lagesen K, Hallin P, Rodland E A, Staerfeldt H H, Rognes T, et    al. (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA    genes. Nucleic Acids Res 35: 3100-3108.-   6. Cantarel B, Korf I, Robb S, et al. (2008) MAKER: An easy-to-use    annotation pipeline designed for emerging model organism genomes.    Genome Research 18: 188-196.-   7. Altschul S F, Madden T L, Schaffer A A, Zhang J, Zhang Z, et    al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein    database search programs. Nucleic Acids Res 25: 3389-3402.-   8. Eddy S R (2009) A new generation of homology search tools based    on probabilistic inference. Genome Inform 23: 205-211.-   9. Haft D H, Selengut J D, White O (2003) The TIGRFAMs database of    protein families. Nucleic Acids Res 31: 371-373.-   10. Tatusov R L, Fedorova N D, Jackson J D, Jacobs A R, Kiryutin B,    et al. (2003) The COG database: an updated version includes    eukaryotes. BMC Bioinformatics 4: 41.-   11. Suzek B E, Huang H, McGarvey P, Mazumder R, Wu C H (2007)    UniRef: comprehensive and non-redundant UniProt reference clusters.    Bioinformatics 23: 1282-1288.-   12. Li H. and Durbin R. (2009) Fast and accurate short read    alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60

The inclusion of various references herein is not to be construed as anyadmission by the Applicants that the references constitute prior art.Applicants expressly reserve their right to challenge any allegations ofunpatentability of inventions disclosed herein over the referencesincluded herein.

Having illustrated and described the principles of the presentinvention, it should be apparent to persons skilled in the art that theinvention can be modified in arrangement and detail without departingfrom such principles.

Although the materials and methods of this invention have been describedin terms of various embodiments and illustrative examples, it will beapparent to those of skill in the art that variations can be applied tothe materials and methods described herein without departing from theconcept, spirit and scope of the invention. All such similar substitutesand modifications apparent to those skilled in the art are deemed to bewithin the spirit, scope and concept of the invention as defined by theappended claims.

What is claimed is:
 1. A method for improving lettuce production, saidmethod comprising applying a coating or partial coating of a compositioncomprising Methylobacterium to a lettuce plant, a part thereof, or to alettuce seed, wherein said composition comprises: (i) a solid substancewith adherent Methylobacterium grown thereon; (ii) an emulsion havingMethylobacterium grown therein; (iii) aMethylobacterium is selected fromthe group consisting of NLS0017 (NRRL B-50931), NLS0020 (NRRL B-50930),NLS0021 (NRRL B-50939), NLS0037 (NRRL B-50941), NLS0038 (NRRL B-50942),NLS0042 (NRRL B-50932), NLS0046 (NRRL B-50929), NLS0062 (NRRL B-50937),NLS0064 (NRRL B-50938), NLS0065 (NRRL B-50935), NLS0066 (NRRL B-50940),NLS0068 (NRRL B-50934), NLS0069 (NRRL B-50936), NLS0089 (NRRL B-50933),and derivatives thereof and an agriculturally acceptable adjuvant,excipient, or combination thereof; or (iv) aMethylobacterium that has atleast one gene encoding at least one protein that is orthologous to aprotein having an amino acid sequence of SEQ ID NO: 1-5125 thereof andan agriculturally acceptable adjuvant, excipient, or combinationthereof; and wherein said lettuce plant or lettuce plant grown from saidseed exhibits a trait improvement selected from the group consisting ofan increased rate of leaf growth, an increased rate of root growth,increased total biomass production, increased seed yield, decreasedcycle time, and combinations thereof when compared to an untreatedcontrol lettuce plant or a control lettuce plant grown from an untreatedseed, thereby obtaining improved lettuce production.
 2. The method ofclaim 1, wherein said composition comprises Methylobacterium at a titerof about 1×10⁶ CFU/gm to about 1×10¹¹ CFU/gm for a solid composition orat a titer of about 1×10⁶ CFU/mL to about 1×10¹¹ CFU/mL for a liquidcomposition containing the solid substance or for the emulsion.
 3. Themethod of claim 1, wherein said Methylobacterium of (i) or (ii) has atleast one gene encoding at least one protein that is orthologous to aprotein having an amino acid sequence of SEQ ID NO: 1-5125.
 4. Themethod of claim 3, wherein the Methylobacterium has at least one geneencoding a protein that is orthologous to a reference protein of Table7.
 5. The method of claim 4, wherein the composition is applied to alettuce plant or a part thereof and wherein the reference protein ofTable 7 is selected from the group consisting of SEQ ID NO: 13, 14, 23,1094, 1100, 1106, 2467, 2468, 3357, 3370, and/or
 3968. 6. The method ofclaim 1, wherein the composition is applied to a lettuce seed and theMethylobacterium is selected from the group consisting of NLS0017 (NRRLB-50931), NLS0020 (NRRL B-50930), NLS0021 (NRRL B-50939), NLS0037 (NRRLB-50941), NLS0038 (NRRL B-50942), NLS0042 (NRRL B-50932), NLS0046 (NRRLB-50929), NLS0062 (NRRL B-50937), NLS0064 (NRRL B-50938), NLS0065 (NRRLB-50935), NLS0066 (NRRL B-50940), NLS0068 (NRRL B-50934), NLS0069 (NRRLB-50936), NLS0089 (NRRL B-50933), and derivatives thereof.
 7. The methodof claim 1, wherein the composition is applied to a lettuce plant or apart thereof and the Methylobacterium is selected from the groupconsisting of NLS0017 (NRRL B-50931), NLS0020 (NRRL B-50930), NLS0021(NRRL B-50939), NLS0037 (NRRL B-50941), NLS0038 (NRRL B-50942), NLS0042(NRRL B-50932), NLS0046 (NRRL B-50929), NLS0062 (NRRL B-50937), NLS0064(NRRL B-50938), NLS0065 (NRRL B-50935), NLS0066 (NRRL B-50940), NLS0068(NRRL B-50934), NLS0069 (NRRL B-50936), NLS0089 (NRRL B-50933), andderivatives thereof.
 8. The method of claim 1, wherein said appliedcomposition coats or partially coats said plant or a part thereof, orsaid seed.
 9. The method of claim 1, wherein the method furthercomprises: (i) growing said lettuce plant or lettuce plant grown fromsaid seed; and/or (ii) harvesting leaves or seed from said lettuce plantor lettuce plant grown from said seed.
 10. The method of claim 1,wherein the solid substance with adherent Methylobacterium is not asubstance that promotes growth of resident microorganisms on the lettuceplant, the part thereof, or the lettuce seed.
 11. The method of claim 1,wherein the composition comprises an agriculturally acceptable adjuvantand/or excipient.
 12. The method of any one of claims 1-11, wherein saidcomposition is depleted of substances that promote growth of residentmicroorganisms on said plant or seed.
 13. A method for improving lettuceplant production, said method comprising applying a compositioncomprising Methylobacterium to a lettuce plant, a part thereof, orlettuce seed, wherein said composition is depleted of substances thatpromote growth of resident microorganisms on said plant or seed andwherein said plant or plant grown from said seed exhibits a traitimprovement selected from the group consisting of an increased rate ofleaf growth, an increased rate of root growth, increased total biomassproduction, increased seed yield, decreased cycle time, and combinationsthereof when compared to an untreated control lettuce plant or a controllettuce plant grown from an untreated seed thereby obtaining improvedlettuce plant production.
 14. The method of claim 13, wherein saidcomposition comprises a solid substance with adherent Methylobacteriumgrown thereon.
 15. The method of claim 13, wherein the solid substanceis not a substance that promotes growth of resident microorganisms onthe lettuce plant, the part thereof, or the lettuce seed.
 16. The methodof claim 14, wherein the composition comprises Methylobacterium at atiter of about 1×10⁶ CFU/gm to about 1×10¹⁴ CFU/gm.
 17. The method ofclaim 13, wherein said composition comprises a liquid, a solid substancewith Methylobacterium adhered thereto in a liquid, a solid substancewith Methylobacterium adhered thereto in an emulsion, or an emulsion.18. The method of claim 17, wherein said composition comprisesMethylobacterium at a titer of about 1×10⁶ CFU/mL to about 1×10¹¹CFU/mL.
 19. The method of claim 13, wherein the method furthercomprises: (i) growing said lettuce plant or lettuce plant grown fromsaid seed; and/or (ii) harvesting leaves or seed from said lettuce plantor lettuce plant grown from said seed.
 20. The method of claim 13,wherein said Methylobacterium has at least one gene encoding at leastone protein that is orthologous to a protein having an amino acidsequence of SEQ ID NO: 1-5125.
 21. The method of claim 20, wherein saidMethylobacterium has at least one gene encoding a protein that isorthologous to a reference protein of Table
 7. 22. The method of claim20, wherein the reference protein of Table 7 is selected from the groupconsisting of SEQ ID NO: 13, 14, 23, 1094, 1100, 1106, 2467, 2468, 3357,3370, and/or
 3968. 23. The method of claim 13, wherein the compositionis applied to a lettuce seed and the Methylobacterium is selected fromthe group consisting of NLS0017 (NRRL B-50931), NLS0020 (NRRL B-50930),NLS0021 (NRRL B-50939), NLS0037 (NRRL B-50941), NLS0038 (NRRL B-50942),NLS0042 (NRRL B-50932), NLS0046 (NRRL B-50929), NLS0062 (NRRL B-50937),NLS0064 (NRRL B-50938), NLS0065 (NRRL B-50935), NLS0066 (NRRL B-50940),NLS0068 (NRRL B-50934), NLS0069 (NRRL B-50936), NLS0089 (NRRL B-50933),and derivatives thereof.
 24. The method of claim 13, wherein thecomposition is applied to a lettuce plant or a part thereof and theMethylobacterium is selected from the group consisting of NLS0042,NLS0017, NLS0020, and NLS0068.
 25. The method of any one of claims 13 to24, wherein said composition coats or partially coats said plant or apart thereof, or said seed.
 26. A composition comprising: (a) (i) asolid substance with adherent Methylobacterium grown thereon; (ii) anemulsion with Methylobacterium grown therein; or (iii) aMethylobacterium that has at least one gene encoding a protein that isorthologous to a protein having an amino acid sequence of SEQ ID NO:1-5125; and (b) an agriculturally acceptable excipient, adjuvant, orcombination thereof.
 27. The composition of claim 26, wherein thewherein said Methylobacterium has at least one gene encoding a proteinthat is orthologous to a reference protein of Table
 7. 28. Thecomposition of claim 27, wherein the reference protein is selected fromthe group consisting of SEQ ID NO: 13, 14, 23, 1094, 1100, 1106, 2467,2468, 3357, 3370, and/or
 3968. 29. The composition of claim 26, whereinthe Methylobacterium is selected from the group consisting of NLS0017(NRRL B-50931), NLS0020 (NRRL B-50930), NLS0037 (NRRL B-50941), NLS0042(NRRL B-50932), NLS0065 (NRRL B-50935), NLS0066 (NRRL B-50940), andderivatives thereof.
 30. The composition of claim 26, wherein thecomposition is depleted of substances that promote growth of residentmicroorganisms on a plant or seed.
 31. The composition of claim 30,wherein said substance that promotes growth of resident microorganismson a plant or seed is selected from the group consisting of a carbonsource, a nitrogen source, a phosphorous source, a sulfur source, amagnesium source, and combinations thereof.
 32. The composition of claim26, further comprising an agriculturally acceptable adjuvant and/orexcipient.
 33. The composition of claim 31, wherein the solid substancewith adherent Methylobacterium grown thereon has a Methylobacteriumtiter of at least about 5×10⁸ CFU/gm to at least about 1×10¹⁴ CFU/gm.34. The composition of claim 29, wherein the Methylobacterium isselected from the group consisting of NLS0017 (NRRL B-50931), NLS0020(NRRL B-50930), NLS0037 (NRRL B-50941), NLS0042 (NRRL B-50932), NLS0065(NRRL B-50935), and NLS0066 (NRRL B-50940).
 35. The composition of anyone of claims 26-34, wherein the composition is adapted for use intreating a plant or seed.
 36. A lettuce plant part or lettuce seed thatis coated or partially coated with the composition of any one of claims26-34.
 37. A lettuce plant part or lettuce seed that is coated orpartially coated with a composition comprising Methylobacterium, whereinthe lettuce plant part or lettuce seed is obtained by the methoddescribed in any one of claim 1-11 or 13-24.
 38. An isolatedMethylobacterium selected from the group consisting of NLS0017 (NRRLB-50931), NLS0020 (NRRL B-50930), NLS0021 (NRRL B-50939), NLS0037 (NRRLB-50941), NLS0038 (NRRL B-50942), NLS0042 (NRRL B-50932), NLS0046 (NRRLB-50929), NLS0062 (NRRL B-50937), NLS0064 (NRRL B-50938), NLS0065 (NRRLB-50935), NLS0066 (NRRL B-50940), NLS0068 (NRRL B-50934), NLS0069 (NRRLB-50936), NLS0089 (NRRL B-50933), and derivatives thereof.
 39. Acomposition comprising: (i) an isolated Methylobacterium selected fromthe group consisting of NLS0017 (NRRL B-50931), NLS0020 (NRRL B-50930),NLS0021 (NRRL B-50939), NLS0037 (NRRL B-50941), NLS0038 (NRRL B-50942),NLS0042 (NRRL B-50932), NLS0046 (NRRL B-50929), NLS0062 (NRRL B-50937),NLS0064 (NRRL B-50938), NLS0065 (NRRL B-50935), NLS0066 (NRRL B-50940),NLS0068 (NRRL B-50934), NLS0069 (NRRL B-50936), NLS0089 (NRRL B-50933),derivatives thereof and (ii) an agriculturally acceptable adjuvant,excipient, or combination thereof.
 40. A lettuce plant, lettuce plantpart, or lettuce seed that is coated with the composition of claim 39.